diff --git a/.github/workflows/merge-gate.yml b/.github/workflows/merge-gate.yml
index e707ce0eef..9260adea1e 100644
--- a/.github/workflows/merge-gate.yml
+++ b/.github/workflows/merge-gate.yml
@@ -83,7 +83,7 @@ jobs:
             make install
             cd ..
             export PATH=$HOME/bin:$PATH
-            export LD_LIBRARY_PATH=$HOME/lib:$PATH
+            export LD_LIBRARY_PATH=$HOME/lib:$LD_LIBRARY_PATH
             export DO_PARALLEL="mpirun -n 2"
             if [ $USE_OPENMP = "yes" ]; then
               export OMP_NUM_THREADS=1
diff --git a/configure b/configure
index b635608b99..38282377c9 100755
--- a/configure
+++ b/configure
@@ -2342,10 +2342,7 @@ EOF
       CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"
     fi
   fi
-  # ----- Mac OSX --------------------------------
-  if [ "$PLATFORM" = 'Darwin' ] ; then
-    SHARED_SUFFIX='.dylib'
-    if [ "$COMPILERS" = 'clang' ] ; then
+  if [ "$COMPILERS" = 'clang' ] ; then
       # On OSX with clang, some libraries may be built with libstdc++ and will
       # fail to link without this flag.
       cat > testp.cpp <<EOF
@@ -2358,7 +2355,7 @@ EOF
         # Test with stdlib flag
         TestProgram quiet "With stdlib flag" "$CXX" "$CXXFLAGS" testp.cpp "-stdlib=libstdc++"
         if [ $? -eq 1 ] ; then
-          Err "Could not link properly with clang++ on OSX"
+          Err "Could not link libstdc++ properly with clang++"
         fi
         LDFLAGS="$LDFLAGS -stdlib=libstdc++"
       fi
@@ -2409,7 +2406,11 @@ EOF
         fi
         echo "OK"
       fi
-    fi # End if clang
+  fi # End if clang
+  # ----- Mac OSX --------------------------------
+  if [ "$PLATFORM" = 'Darwin' ] ; then
+    SHARED_SUFFIX='.dylib'
+
   # ----- Windows/Cygwin -------------------------
   elif [ "$PLATFORM" = 'windows' ] ; then
     SHARED_SUFFIX='.dll.a'
diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx
index b1c11b0368..e2bf82d411 100644
--- a/doc/cpptraj.lyx
+++ b/doc/cpptraj.lyx
@@ -2992,6 +2992,11 @@ phipsi.dat
 #Frame   phi   psi
 \end_layout
 
+\begin_layout Standard
+Note that when reading the Amber Prep and Amber OFF Library formats, a COORDS
+ data set will be created for each unit present in these files.
+\end_layout
+
 \begin_layout Standard
 \begin_inset Float table
 wide false
@@ -3001,7 +3006,7 @@ status open
 \begin_layout Plain Layout
 \align center
 \begin_inset Tabular
-<lyxtabular version="3" rows="20" columns="5">
+<lyxtabular version="3" rows="22" columns="5">
 <features tabularvalignment="middle">
 <column alignment="center" valignment="top" width="20text%">
 <column alignment="center" valignment="top" width="20text%">
@@ -3912,7 +3917,7 @@ Used for cluster analysis.
 </cell>
 </row>
 <row>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
 \begin_inset Text
 
 \begin_layout Plain Layout
@@ -3921,7 +3926,7 @@ NetCDF Data
 
 \end_inset
 </cell>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
 \begin_inset Text
 
 \begin_layout Plain Layout
@@ -3930,7 +3935,7 @@ NetCDF Data
 
 \end_inset
 </cell>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
 \begin_inset Text
 
 \begin_layout Plain Layout
@@ -3939,7 +3944,7 @@ netcdf
 
 \end_inset
 </cell>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
 \begin_inset Text
 
 \begin_layout Plain Layout
@@ -3948,13 +3953,107 @@ All data
 
 \end_inset
 </cell>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
 \begin_inset Text
 
 \begin_layout Plain Layout
 Only state info saved for pH data.
 \end_layout
 
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Amber Prep File
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+.prepin
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+prepin
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+COORDS
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Read Only
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Amber OFF Library File
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+.off, .lib
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+off,lib
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+COORDS
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Read Only
+\end_layout
+
 \end_inset
 </cell>
 </row>
@@ -6253,7 +6352,7 @@ The following COORDS data set commands are available:
 \begin_layout Standard
 \align center
 \begin_inset Tabular
-<lyxtabular version="3" rows="17" columns="2">
+<lyxtabular version="3" rows="19" columns="2">
 <features tabularvalignment="middle">
 <column alignment="center" valignment="top" width="25text%">
 <column alignment="center" valignment="top" width="75text%">
@@ -6585,7 +6684,27 @@ Rotate specified dihedral to specified value or by given increment.
 </cell>
 </row>
 <row>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+sequence
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Create a new molecule from a sequence of COORDS sets.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
 \begin_inset Text
 
 \begin_layout Plain Layout
@@ -6594,13 +6713,34 @@ splitcoords
 
 \end_inset
 </cell>
-<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
 \begin_inset Text
 
 \begin_layout Plain Layout
 Split molecules in a COORDS set into a trajectory.
 \end_layout
 
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+zmatrix
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" bottomline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Apply Z-matrix to a COORDS set or calculate Z-matrix for a molecule/frame
+ in a COORDS set.
+\end_layout
+
 \end_inset
 </cell>
 </row>
@@ -7487,19 +7627,17 @@ graft
 \end_layout
 
 \begin_layout LyX-Code
-graft src <source COORDS> [srcframe <#>] [srcfitmask <mask>] [srcmask <mask>]
+graft src <source COORDS> [srcframe <#>] [srcmask <srcmask> [srccharge <srccharg
+e>]]
 \end_layout
 
 \begin_layout LyX-Code
-      srccharge <charge>
-\end_layout
-
-\begin_layout LyX-Code
-  	tgt <target COORDS> [tgtframe <#>] [tgtfitmask <mask>] [tgtmask <mask>]
+  	tgt <target COORDS> [tgtframe <#>] [tgtmask <tgtmask> [tgtcharge <tgtcharge>]
+]
 \end_layout
 
 \begin_layout LyX-Code
-      tgtcharge <charge>
+      {ic | [srcfitmask <srcmask>] [tgtfitmask <tgtmask>]}
 \end_layout
 
 \begin_layout LyX-Code
@@ -7527,14 +7665,6 @@ COORDS> Source coordinates.
 <#>] Frame # from source coordinates to use (default 1).
 \end_layout
 
-\begin_layout Description
-[srcfitmask
-\begin_inset space ~
-\end_inset
-
-<mask>] Atoms from source to use if RMS-fitting source onto target.
-\end_layout
-
 \begin_layout Description
 [srcmask
 \begin_inset space ~
@@ -7543,6 +7673,7 @@ COORDS> Source coordinates.
 <mask>] Atoms to keep from source (default all).
 \end_layout
 
+\begin_deeper
 \begin_layout Description
 [srccharge
 \begin_inset space ~
@@ -7552,6 +7683,7 @@ COORDS> Source coordinates.
  atoms equals <charge> via scaling.
 \end_layout
 
+\end_deeper
 \begin_layout Description
 tgt
 \begin_inset space ~
@@ -7573,28 +7705,42 @@ COORDS> Target coordinates that will be grafted onto.
 \end_layout
 
 \begin_layout Description
-[tgtfitmask
+[tgtmask
 \begin_inset space ~
 \end_inset
 
-<mask>] Atoms from target to use if RMS-fitting source onto target.
+<mask>] Atoms to keep from target (default all).
 \end_layout
 
+\begin_deeper
 \begin_layout Description
-[tgtmask
+[tgtcharge
 \begin_inset space ~
 \end_inset
 
-<mask>] Atoms to keep from target (default all).
+<charge>] If trimming atoms from target, ensure sum of charges on remaining
+ atoms equals <charge> via scaling.
 \end_layout
 
+\end_deeper
 \begin_layout Description
-[tgtcharge
+[ic] Connect source and target using internal coordinates.
+\end_layout
+
+\begin_layout Description
+[srcfitmask
 \begin_inset space ~
 \end_inset
 
-<charge>] If trimming atoms from target, ensure sum of charges on remaining
- atoms equals <charge> via scaling.
+<mask>] Atoms from source to use if RMS-fitting source onto target.
+\end_layout
+
+\begin_layout Description
+[tgtfitmask
+\begin_inset space ~
+\end_inset
+
+<mask>] Atoms from target to use if RMS-fitting source onto target.
 \end_layout
 
 \begin_layout Description
@@ -7616,7 +7762,8 @@ COORDS> Name of output COORDS set containing source grafted onto target.
 
 <tgt>,<src>] Create a bond between target atom selected by <tgt> and source
  atoms selected by <src> in the final structure.
- May be specified multiple times.
+ Must be specified only once if connecting via internal coordinates, otherwise
+ may be specified multiple times.
 \end_layout
 
 \end_deeper
@@ -7647,6 +7794,8 @@ bond
 \series default
  keyword can be used to create bonds between target and source in the final
  structure.
+ If using internal coordinates to connect the units, exactly one bond must
+ be specified.
 \end_layout
 
 \begin_layout Subsection
@@ -8834,6 +8983,147 @@ rotatedihedral crdset TZ2 value 35 res 8 type chip
 crdout TZ2 tz2.rotate.1.mol2
 \end_layout
 
+\begin_layout Subsection
+sequence
+\begin_inset CommandInset label
+LatexCommand label
+name "subsec:cpptraj-sequence"
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout LyX-Code
+sequence name <output set name> <unit0> <unit1> ...
+\end_layout
+
+\begin_layout LyX-Code
+         [{libset <libsetname>} ...]
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+name
+\begin_inset space ~
+\end_inset
+
+<output
+\begin_inset space ~
+\end_inset
+
+set
+\begin_inset space ~
+\end_inset
+
+name> Name of final molecule.
+\end_layout
+
+\begin_layout Description
+<unit0>
+\begin_inset space ~
+\end_inset
+
+<unit1> Name of COORDS set (with connection info).
+\end_layout
+
+\begin_layout Description
+[{libset
+\begin_inset space ~
+\end_inset
+
+<libsetname>}
+\begin_inset space ~
+\end_inset
+
+...} One or more set name prefixes of data sets (libraries) containing units.
+\end_layout
+
+\begin_layout Standard
+Data sets created:
+\end_layout
+
+\begin_layout Description
+<output
+\begin_inset space ~
+\end_inset
+
+set
+\begin_inset space ~
+\end_inset
+
+name> COORDS set containing final molecule.
+\end_layout
+
+\end_deeper
+\begin_layout Standard
+Connect units in different COORDS sets together to form a single molecule.
+ Internal coordinates are used to try to determine the correct geometry
+ around connection sites.
+ The COORDS sets must have connection information set, either from reading
+ in an Amber OFF library file or set manually via 
+\series bold
+\emph on
+dataset
+\series default
+\emph default
+ 
+\series bold
+connect
+\series default
+ (see 
+\begin_inset CommandInset ref
+LatexCommand vref
+reference "subsec:cpptraj-datasetcmd"
+plural "false"
+caps "false"
+noprefix "false"
+
+\end_inset
+
+).
+\end_layout
+
+\begin_layout Standard
+For example, the following reads in two Mol2 files as COORDS sets, sets
+ up connection atoms, then creates a molecule via 
+\series bold
+\emph on
+sequence:
+\end_layout
+
+\begin_layout LyX-Code
+parm MOC.mol2
+\end_layout
+
+\begin_layout LyX-Code
+loadcrd MOC.mol2 parm MOC.mol2 name MOC
+\end_layout
+
+\begin_layout LyX-Code
+dataset connect MOC tailmask @O5
+\end_layout
+
+\begin_layout LyX-Code
+parm CNALA.mol2 
+\end_layout
+
+\begin_layout LyX-Code
+loadcrd CNALA.mol2 parm CNALA.mol2 name CNALA
+\end_layout
+
+\begin_layout LyX-Code
+dataset connect CNALA headmask @N
+\end_layout
+
+\begin_layout LyX-Code
+sequence MOC CNALA name Mol
+\end_layout
+
+\begin_layout LyX-Code
+crdout Mol Mol.mol2
+\end_layout
+
 \begin_layout Subsection
 splitcoords
 \end_layout
@@ -8887,6 +9177,141 @@ Set0
 splitcoords Set0 name Set0Split
 \end_layout
 
+\begin_layout Subsection
+zmatrix
+\end_layout
+
+\begin_layout LyX-Code
+zmatrix <COORDS set name> [name <output set name>]
+\end_layout
+
+\begin_layout LyX-Code
+        { zset <input zmatrix set> [parm <top>|parmindex <#>] |
+\end_layout
+
+\begin_layout LyX-Code
+          [molnum <mol#>] [frame <frame#>] [out <zmatrix file>] }
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+<COORDS
+\begin_inset space ~
+\end_inset
+
+set
+\begin_inset space ~
+\end_inset
+
+name> COORDS set to calculate Z-matrix from or use as topology for applied
+ Z-matrix.
+\end_layout
+
+\begin_layout Description
+[name
+\begin_inset space ~
+\end_inset
+
+<output
+\begin_inset space ~
+\end_inset
+
+set
+\begin_inset space ~
+\end_inset
+
+name>] Name of output COORDS set (if 'zset') or output Z-matrix set.
+\end_layout
+
+\begin_layout Description
+zset
+\begin_inset space ~
+\end_inset
+
+<input
+\begin_inset space ~
+\end_inset
+
+zmatrix
+\begin_inset space ~
+\end_inset
+
+set> Name of Z-matrix set to use to generate coordinates.
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+parm
+\begin_inset space ~
+\end_inset
+
+<top> Use specified topology name as topology for generated coordinates.
+\end_layout
+
+\begin_layout Description
+parmindex
+\begin_inset space ~
+\end_inset
+
+<#> Use topology index as topology for generated coordinates.
+\end_layout
+
+\end_deeper
+\begin_layout Description
+[molnum
+\begin_inset space ~
+\end_inset
+
+<mol#>] Calculate Z-matrix from specified molecule (default first molecule).
+\end_layout
+
+\begin_layout Description
+[frame
+\begin_inset space ~
+\end_inset
+
+<frame#>] Calculate Z-matrix from specified molecule in specified frame
+ (default first frame).
+\end_layout
+
+\begin_layout Description
+[out
+\begin_inset space ~
+\end_inset
+
+<zmatrix
+\begin_inset space ~
+\end_inset
+
+file>] File to write calculated Z-matrix to.
+\end_layout
+
+\begin_layout Standard
+Data sets created:
+\end_layout
+
+\begin_layout Description
+<output
+\begin_inset space ~
+\end_inset
+
+set
+\begin_inset space ~
+\end_inset
+
+name> If 'zset', COORDS set containing final coordinates.
+ Otherwise contains Z-matrix data.
+\end_layout
+
+\end_deeper
+\begin_layout Standard
+Command for working with Z-matrices.
+ If 'zset' is specified, generate coordinates from the specified Z-matrix
+ data set and topology.
+ Otherwise, calculate a Z-matrix for a single molecule from the specified
+ frame of given COORDS data set.
+\end_layout
+
 \begin_layout Section
 General Commands
 \end_layout
@@ -10073,6 +10498,13 @@ reference "subsec:cpptraj-filter"
 
 \begin_layout Subsection
 dataset
+\begin_inset CommandInset label
+LatexCommand label
+name "subsec:cpptraj-datasetcmd"
+
+\end_inset
+
+
 \end_layout
 
 \begin_layout LyX-Code
@@ -10111,6 +10543,11 @@ dataset { legend <legend> <set> |
  |
 \end_layout
 
+\begin_layout LyX-Code
+          connect {[head <head atom>] [tail <tail atom>]|[headmask <headmask>]
+ [tailmask <tailmask>]}
+\end_layout
+
 \begin_layout LyX-Code
           dim {xdim|ydim|zdim|ndim <#>} [label <label>] [min <min>] [step
  <step>] |
@@ -10395,6 +10832,73 @@ selection>] Remove data sets from <set selection> according to specified
               'greaterthan' '>' 'between' 'outside'
 \end_layout
 
+\begin_layout Description
+connect
+\begin_inset space ~
+\end_inset
+
+<set
+\begin_inset space ~
+\end_inset
+
+args> Add/change connect atom information (used by the sequence command,
+ 
+\begin_inset CommandInset ref
+LatexCommand vref
+reference "subsec:cpptraj-sequence"
+plural "false"
+caps "false"
+noprefix "false"
+
+\end_inset
+
+) to COORDS set(s).
+ Head atoms connect to previous residue, tail atoms connect to next residue.
+ Can use either absolute atom numbers or atom mask expressions.
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+[head
+\begin_inset space ~
+\end_inset
+
+<head
+\begin_inset space ~
+\end_inset
+
+atom>]
+\begin_inset space ~
+\end_inset
+
+[tail
+\begin_inset space ~
+\end_inset
+
+<tail
+\begin_inset space ~
+\end_inset
+
+atom>] Specify the head/tail atoms by atom number.
+\end_layout
+
+\begin_layout Description
+[headmask
+\begin_inset space ~
+\end_inset
+
+<headmask>]
+\begin_inset space ~
+\end_inset
+
+[tailmask
+\begin_inset space ~
+\end_inset
+
+<tailmask>] Specify the head/tail atoms by atom mask.
+\end_layout
+
+\end_deeper
 \begin_layout Description
 dim
 \begin_inset space ~
@@ -10603,7 +11107,7 @@ pucker
 \end_layout
 
 \begin_layout Standard
-Options for type noe only:
+Options for 'type noe' only:
 \end_layout
 
 \begin_layout Description
diff --git a/src/Action_Distance.cpp b/src/Action_Distance.cpp
index 83d0303f14..054497d20a 100644
--- a/src/Action_Distance.cpp
+++ b/src/Action_Distance.cpp
@@ -1,6 +1,7 @@
 #include "Action_Distance.h"
 #include "CpptrajStdio.h"
 #include "DistRoutines.h"
+#include "AssociatedData_NOE.h"
 
 // CONSTRUCTOR
 Action_Distance::Action_Distance() :
@@ -35,7 +36,7 @@ Action::RetType Action_Distance::Init(ArgList& actionArgs, ActionInit& init, int
   std::string stypename = actionArgs.GetStringKey("type");
   if ( stypename == "noe" ) {
     stype = MetaData::NOE;
-    if (noe.NOE_Args( actionArgs )) return Action::ERR;
+    if (noe.ProcessAdataArgs( actionArgs )) return Action::ERR;
   }
   // Determine mode.
   ReferenceFrame refFrm = init.DSL().GetReferenceFrame( actionArgs );
diff --git a/src/Action_NMRrst.cpp b/src/Action_NMRrst.cpp
index 5f33fc0912..868077390a 100644
--- a/src/Action_NMRrst.cpp
+++ b/src/Action_NMRrst.cpp
@@ -10,6 +10,7 @@
 #include "ViewRst.h"
 #include "BufferedLine.h"
 #include "DistRoutines.h"
+#include "AssociatedData_NOE.h"
 
 // CONSTRUCTOR
 Action_NMRrst::Action_NMRrst() :
diff --git a/src/Analysis_Statistics.cpp b/src/Analysis_Statistics.cpp
index 672a50ffbc..2fbd0666b8 100644
--- a/src/Analysis_Statistics.cpp
+++ b/src/Analysis_Statistics.cpp
@@ -1,6 +1,7 @@
 #include <cmath> // sqrt
 #include "Analysis_Statistics.h"
 #include "CpptrajStdio.h"
+#include "AssociatedData_NOE.h"
 
 // CONSTRUCTOR
 Analysis_Statistics::Analysis_Statistics() :
diff --git a/src/AssociatedData.h b/src/AssociatedData.h
index 615e9dcc96..f37af22d7c 100644
--- a/src/AssociatedData.h
+++ b/src/AssociatedData.h
@@ -5,30 +5,19 @@ class AssociatedData {
   public:
     /// Destructor. Virtual since this class is inherited.
     virtual ~AssociatedData() {}
-    enum AssociatedType { NOE = 0 };
+    /// Associated data types
+    enum AssociatedType { NOE = 0, CONNECT };
+    /// CONSTRUCTOR - take associated data type
     AssociatedData(AssociatedType t) : type_(t) {}
+    /// \return Associated data type
     AssociatedType Type() { return type_; }
+    /// \return A copy of the associated data
     virtual AssociatedData* Copy() const = 0;
+    /// Print associated data info to stdout
+    virtual void Ainfo() const = 0;
+    /// Process arguments for associated data
+    virtual int ProcessAdataArgs(ArgList&) = 0;
   private:
     AssociatedType type_;
 };
-
-/// For Analysis_Statistics DISTANCE NOE
-class AssociatedData_NOE : public AssociatedData {
-  public:
-    AssociatedData_NOE() : AssociatedData(NOE), l_bound_(0.0), u_bound_(0.0), rexp_(-1.0) {}
-    AssociatedData_NOE(double l, double u, double r) :
-      AssociatedData(NOE), l_bound_(l), u_bound_(u), rexp_(r) {}
-    static const char* HelpText;
-    int NOE_Args(ArgList&);
-    double NOE_bound()  const { return l_bound_;  }
-    double NOE_boundH() const { return u_bound_; }
-    double NOE_rexp()   const { return rexp_;   }
-
-    AssociatedData* Copy() const { return new AssociatedData_NOE(*this); }
-  private:
-    double l_bound_; ///< Lower bound
-    double u_bound_; ///< Upper bound
-    double rexp_;    ///< Expected distance
-};
 #endif
diff --git a/src/AssociatedData_Connect.cpp b/src/AssociatedData_Connect.cpp
new file mode 100644
index 0000000000..469e531088
--- /dev/null
+++ b/src/AssociatedData_Connect.cpp
@@ -0,0 +1,38 @@
+#include "AssociatedData_Connect.h"
+#include "CpptrajStdio.h"
+#include "ArgList.h"
+
+/** CONSTRUCTOR - head and tail atom */
+AssociatedData_Connect::AssociatedData_Connect(int head, int tail) :
+  AssociatedData(CONNECT)
+{
+  connect_.push_back( head );
+  connect_.push_back( tail );
+}
+
+const char* AssociatedData_Connect::HelpText = "[head <head atom>] [tail <tail atom>]";
+
+int AssociatedData_Connect::ProcessAdataArgs(ArgList& argIn) {
+  // Expect user atom args to start from 1
+  int head = argIn.getKeyInt("head", 0) - 1;
+  int tail = argIn.getKeyInt("tail", 0) - 1;
+  if (head < 0) head = -1;
+  if (tail < 0) tail = -1;
+  if (head == -1 && tail == -1) {
+    mprinterr("Error: Either at least 'head' or 'tail' must be specified.\n");
+    return 1;
+  }
+  connect_.push_back( head );
+  connect_.push_back( tail );
+  return 0;
+}
+
+void AssociatedData_Connect::Ainfo() const {
+  if (!connect_.empty()) {
+    mprintf(" (Connect Atoms:");
+    for (Iarray::const_iterator it = connect_.begin(); it != connect_.end(); ++it)
+      mprintf(" %i", *it + 1);
+    mprintf(")");
+  }
+  return;
+}
diff --git a/src/AssociatedData_Connect.h b/src/AssociatedData_Connect.h
new file mode 100644
index 0000000000..400c0dc7c2
--- /dev/null
+++ b/src/AssociatedData_Connect.h
@@ -0,0 +1,26 @@
+#ifndef INC_ASSOCIATEDDATA_CONNECT_H
+#define INC_ASSOCIATEDDATA_CONNECT_H
+#include <vector>
+#include "AssociatedData.h"
+/// For holding unit connect atoms (COORDS data sets) 
+class AssociatedData_Connect : public AssociatedData {
+    typedef std::vector<int> Iarray;
+  public:
+    /// Empty CONSTRUCTOR
+    AssociatedData_Connect() : AssociatedData(CONNECT) {}
+    /// CONSTRUCTOR - head and tail atom
+    AssociatedData_Connect(int, int);
+    // ----- Inherited functions -------
+    static const char* HelpText;
+    int ProcessAdataArgs(ArgList&);
+    AssociatedData* Copy() const { return new AssociatedData_Connect(*this); }
+    void Ainfo() const;
+    // ---------------------------------
+    void AddConnectAtom(int at) { connect_.push_back( at ); }
+    unsigned int NconnectAtoms() const { return connect_.size(); }
+    Iarray const& Connect() const { return connect_; }
+
+  private:
+    Iarray connect_;
+};
+#endif
diff --git a/src/AssociatedData.cpp b/src/AssociatedData_NOE.cpp
similarity index 79%
rename from src/AssociatedData.cpp
rename to src/AssociatedData_NOE.cpp
index 80f791d13d..912e20b0fe 100644
--- a/src/AssociatedData.cpp
+++ b/src/AssociatedData_NOE.cpp
@@ -1,11 +1,11 @@
-#include "AssociatedData.h"
+#include "AssociatedData_NOE.h"
 #include "CpptrajStdio.h"
 #include "ArgList.h"
 
 const char* AssociatedData_NOE::HelpText = 
   "[bound <lower> bound <upper>] [rexp <expected>] [noe_strong] [noe_medium] [noe_weak]";
 
-int AssociatedData_NOE::NOE_Args(ArgList& argIn) {
+int AssociatedData_NOE::ProcessAdataArgs(ArgList& argIn) {
   l_bound_ = argIn.getKeyDouble("bound", 0.0);
   u_bound_ = argIn.getKeyDouble("bound", 0.0);
   rexp_ = argIn.getKeyDouble("rexp", -1.0);
@@ -26,3 +26,7 @@ int AssociatedData_NOE::NOE_Args(ArgList& argIn) {
   }
   return 0;
 }
+
+void AssociatedData_NOE::Ainfo() const {
+  mprintf("(NOE %g < %g < %g)", l_bound_, rexp_, u_bound_);
+}
diff --git a/src/AssociatedData_NOE.h b/src/AssociatedData_NOE.h
new file mode 100644
index 0000000000..8da077db90
--- /dev/null
+++ b/src/AssociatedData_NOE.h
@@ -0,0 +1,27 @@
+#ifndef INC_ASSOCIATEDDATA_NOE_H
+#define INC_ASSOCIATEDDATA_NOE_H
+#include "AssociatedData.h"
+class ArgList;
+/// For Analysis_Statistics DISTANCE NOE
+class AssociatedData_NOE : public AssociatedData {
+  public:
+    /// Empty CONSTRUCTOR
+    AssociatedData_NOE() : AssociatedData(NOE), l_bound_(0.0), u_bound_(0.0), rexp_(-1.0) {}
+    /// CONSTRUCTOR - take lower/upper bounds and expected distance
+    AssociatedData_NOE(double l, double u, double r) :
+      AssociatedData(NOE), l_bound_(l), u_bound_(u), rexp_(r) {}
+    // ----- Inherited functions -------
+    static const char* HelpText;
+    int ProcessAdataArgs(ArgList&);
+    AssociatedData* Copy() const { return new AssociatedData_NOE(*this); }
+    void Ainfo() const;
+    // ---------------------------------
+    double NOE_bound()  const { return l_bound_;  }
+    double NOE_boundH() const { return u_bound_; }
+    double NOE_rexp()   const { return rexp_;   }
+  private:
+    double l_bound_; ///< Lower bound
+    double u_bound_; ///< Upper bound
+    double rexp_;    ///< Expected distance
+};
+#endif
diff --git a/src/Atom.cpp b/src/Atom.cpp
index bb4b7e1199..15f8500181 100644
--- a/src/Atom.cpp
+++ b/src/Atom.cpp
@@ -136,6 +136,11 @@ void Atom::DetermineElement(int atomicnum) {
     SetElementFromName();
 }
 
+/** Set atomic mass from current element */
+void Atom::SetMassFromElement() {
+  mass_ = AtomicElementMass_[ element_ ];
+}
+
 // CONSTRUCTOR
 Atom::Atom(NameType const& aname, double charge, double mass, NameType const& atype) :
   charge_(charge), polar_(0.0), mass_(mass), gb_radius_(0.0), gb_screen_(0.0),
diff --git a/src/Atom.h b/src/Atom.h
index e5b94a2a3f..ddc79dad78 100644
--- a/src/Atom.h
+++ b/src/Atom.h
@@ -97,6 +97,8 @@ class Atom {
     double ParseRadius() const;
     /// Determine element from given atomic number. Use mass/name if number < 1.
     void DetermineElement(int);
+    /// Set atomic mass from current element
+    void SetMassFromElement();
   protected:
     static const size_t NUMELEMENTS_ = 77;
   private:
diff --git a/src/Chirality.h b/src/Chirality.h
deleted file mode 100644
index 01e02db151..0000000000
--- a/src/Chirality.h
+++ /dev/null
@@ -1,17 +0,0 @@
-#ifndef INC_CHIRALITY_H
-#define INC_CHIRALITY_H
-class Topology;
-class Frame;
-namespace Cpptraj {
-namespace Chirality {
-
-enum ChiralType { ERR = 0, IS_S, IS_R };
-
-/// \return Chirality at specified atom, set torsion value
-ChiralType DetermineChirality(double&, int, Topology const&, Frame const&, int);
-/// \return Chirality at specified atom
-ChiralType DetermineChirality(int, Topology const&, Frame const&, int);
-
-}
-}
-#endif
diff --git a/src/Command.cpp b/src/Command.cpp
index 2311a4d316..e098f8c9bd 100644
--- a/src/Command.cpp
+++ b/src/Command.cpp
@@ -56,6 +56,8 @@
 #include "Exec_CatCrd.h"
 #include "Exec_CrdTransform.h"
 #include "Exec_ExtendedComparison.h"
+#include "Exec_Zmatrix.h"
+#include "Exec_Sequence.h"
 // ----- TRAJECTORY ------------------------------------------------------------
 #include "Exec_Traj.h"
 // ----- TOPOLOGY --------------------------------------------------------------
@@ -279,7 +281,9 @@ void Command::Init() {
   Command::AddCmd( new Exec_PermuteDihedrals(), Cmd::EXE, 1, "permutedihedrals" );
   Command::AddCmd( new Exec_PrepareForLeap(),   Cmd::EXE, 1, "prepareforleap" );
   Command::AddCmd( new Exec_RotateDihedral(),   Cmd::EXE, 1, "rotatedihedral" );
+  Command::AddCmd( new Exec_Sequence(),         Cmd::EXE, 1, "sequence" );
   Command::AddCmd( new Exec_SplitCoords(),      Cmd::EXE, 1, "splitcoords" );
+  Command::AddCmd( new Exec_Zmatrix(),          Cmd::EXE, 1, "zmatrix" );
   // TRAJECTORY
   Command::AddCmd( new Exec_Ensemble(),     Cmd::EXE, 1, "ensemble" );
   Command::AddCmd( new Exec_EnsembleSize(), Cmd::EXE, 1, "ensemblesize" );
diff --git a/src/DataFile.cpp b/src/DataFile.cpp
index 32c6c44ee2..b215286b34 100644
--- a/src/DataFile.cpp
+++ b/src/DataFile.cpp
@@ -32,6 +32,8 @@
 #include "DataIO_NetCDF.h"
 #include "DataIO_AmberEne.h"
 #include "DataIO_Numpy.h"
+#include "DataIO_AmberPrep.h"
+#include "DataIO_AmberLib.h"
 
 // CONSTRUCTOR
 DataFile::DataFile() :
@@ -85,6 +87,8 @@ const FileTypes::AllocToken DataFile::DF_AllocArray[] = {
 # endif
   { "Amber Energy File",  0,                             0,            DataIO_AmberEne::Alloc},
   { "Numpy array",        0,                             0,            DataIO_Numpy::Alloc},
+  { "Amber Prep File",    DataIO_AmberPrep::ReadHelp,    0,            DataIO_AmberPrep::Alloc},
+  { "Amber OFF File",     0,                             0,            DataIO_AmberLib::Alloc},
   { "Unknown Data file",  0,                       0,                        0                    }
 };
 
@@ -111,6 +115,9 @@ const FileTypes::KeyToken DataFile::DF_KeyArray[] = {
   { PEAKS,        "peaks",        ".peaks" },
   { AMBERENE,     "amberene",     ".ene" },
   { NUMPY,        "numpy",        ".npy" },
+  { AMBERPREP,    "prepin",       ".prepin" },
+  { AMBERLIB,     "off",          ".off" },
+  { AMBERLIB,     "off",          ".lib" },
   { UNKNOWN_DATA, 0,        0        }
 };
 
diff --git a/src/DataFile.h b/src/DataFile.h
index 4571381644..f5f6b0b92a 100644
--- a/src/DataFile.h
+++ b/src/DataFile.h
@@ -18,7 +18,7 @@ class DataFile {
       DATAFILE=0, XMGRACE, GNUPLOT, XPLOR, OPENDX, REMLOG, MDOUT, EVECS,
       VECTRAJ, XVG, CCP4, CHARMMREPD, CHARMMFASTREP,
       CHARMMOUT, CPOUT, CHARMMRTFPRM, CMATRIX_BINARY, CMATRIX_NETCDF, PEAKS,
-      NETCDFDATA, AMBERENE, NUMPY,
+      NETCDFDATA, AMBERENE, NUMPY, AMBERPREP, AMBERLIB,
       UNKNOWN_DATA 
     };
     DataFile();
diff --git a/src/DataIO_AmberLib.cpp b/src/DataIO_AmberLib.cpp
new file mode 100644
index 0000000000..8088f022ea
--- /dev/null
+++ b/src/DataIO_AmberLib.cpp
@@ -0,0 +1,283 @@
+#include "DataIO_AmberLib.h"
+#include "CpptrajStdio.h"
+#include "BufferedLine.h"
+#include "AssociatedData_Connect.h"
+
+/// CONSTRUCTOR
+DataIO_AmberLib::DataIO_AmberLib()
+{
+
+}
+
+// DataIO_AmberLib::ID_DataFormat()
+bool DataIO_AmberLib::ID_DataFormat(CpptrajFile& infile)
+{
+  if (infile.OpenFile()) return false;
+  std::string line = infile.GetLine();
+  infile.CloseFile();
+  bool isLib = (line == "!!index array str");
+
+  return isLib;
+}
+
+// DataIO_AmberLib::ReadHelp()
+void DataIO_AmberLib::ReadHelp()
+{
+
+}
+
+// DataIO_AmberLib::processReadArgs()
+int DataIO_AmberLib::processReadArgs(ArgList& argIn)
+{
+
+  return 0;
+}
+
+// DataIO_AmberLib::ReadData()
+int DataIO_AmberLib::ReadData(FileName const& fname, DataSetList& dsl, std::string const& dsname)
+{
+  BufferedLine infile;
+  if (infile.OpenFileRead( fname )) {
+    mprinterr("Error: Could not open Amber lib file '%s' for reading.\n", fname.full());
+    return 1;
+  }
+
+  // Read first line
+  std::string line = infile.GetLine();
+  if (line != "!!index array str") {
+    mprinterr("Error: Expected first line to be '!!index array str', got '%s'\n", line.c_str());
+    return 1;
+  }
+  typedef std::vector<std::string> Sarray;
+  Sarray UnitNames;
+  // Read units
+  line = infile.GetLine();
+  while (!line.empty() && line[0] != '!')
+  {
+    // Using ArgList here is a hacky way to get rid of the quotes
+    ArgList tmparg(line);
+    UnitNames.push_back( tmparg[0] );
+    line = infile.GetLine();
+  }
+  // Now should be at first unit
+  if (debug_ > 0) mprintf("DEBUG: Units:\n");
+  for (Sarray::const_iterator it = UnitNames.begin(); it != UnitNames.end(); ++it)
+  {
+    if (debug_ > 0) mprintf("DEBUG: Reading unit %s\n", it->c_str());
+    std::string entryColumn = "!entry." + *it + ".unit.atoms";
+    ArgList tmparg( line );
+    if (tmparg.Nargs() < 1 || tmparg[0] != entryColumn) {
+      mprinterr("Error: Expected '%s', got '%s'\n", entryColumn.c_str(), line.c_str());
+      return 1;
+    }
+    DataSet_Coords* ds = (DataSet_Coords*)dsl.AddSet( DataSet::COORDS, MetaData(dsname, *it) );
+    if (ds == 0) {
+      mprinterr("Error: Could not create data set for unit %s\n", it->c_str());
+      return 1;
+    }
+    if (read_unit( ds, infile, line, *it )) {
+      mprinterr("Error: Reading unit '%s'\n", it->c_str());
+      return 1;
+    }
+  }
+  mprintf("\tRead %zu units from Amber OFF file.\n", UnitNames.size());
+
+  return 0;
+}
+
+/** Strings corresponding to SectionType */
+const char* DataIO_AmberLib::sectionStr_[] = {
+  "atoms", "atomspertinfo", "boundbox", "childsequence", "connect",
+  "connectivity", "hierarchy", "name", "positions", "residueconnect",
+  "residues", "solventcap", "velocities", 0 };
+
+/** \return Section type from entry line. */
+DataIO_AmberLib::SectionType DataIO_AmberLib::id_section(std::string const& line,
+                                                         std::string const& unitName)
+{
+  std::string entry = "!entry." + unitName + ".unit.";
+  for (int idx = 0; idx < (int)UNKNOWN_SECTION; idx++) {
+    std::string sectionName = entry + std::string(sectionStr_[idx]);
+    std::size_t found = line.find_first_of(" ");
+    if (found == std::string::npos) {
+      mprinterr("Error: Malformed entry line: %s\n", line.c_str());
+      break;
+    }
+    if (line.compare(0, found, sectionName) == 0)
+      return (SectionType)idx;
+  }
+  return UNKNOWN_SECTION;
+}
+
+/// Remove quotes from string
+static inline std::string noquotes(const char* ptrIn) {
+ std::string out;
+ for (const char* ptr = ptrIn; *ptr != '\0'; ++ptr)
+   if (*ptr != '"')
+     out += *ptr;
+  return out;
+}
+
+/** Read atoms line */
+int DataIO_AmberLib::read_atoms(Topology& topOut, std::string const& line, std::string const& unitName) {
+  // Format: "Atom name" "Type" "Type index (unused)" "resnum" "flags" "sequence" "element" "charge"
+  char aname[16];
+  char atype[16];
+  int typex;
+  int resx;
+  int flags;
+  int seq;
+  int elt;
+  double charge;
+
+  if (sscanf(line.c_str(), "%s %s %i %i %i %i %i %lf",
+             aname, atype, &typex, &resx, &flags, &seq, &elt, &charge) != 8)
+  {
+    mprinterr("Error: Expected 8 columns for atoms table line: %s\n", line.c_str());
+    return 1;
+  }
+  // Sanity check
+  if (seq-1 != topOut.Natom()) {
+    mprinterr("Error: For unit %s expected sequence %i, got %i\n", unitName.c_str(), topOut.Natom()+1, seq);
+    return 1;
+  }
+  Atom atm;
+  atm.SetName( NameType(noquotes(aname)) );
+  atm.SetTypeName( NameType(noquotes(atype)) );
+  atm.DetermineElement( elt );
+  atm.SetMassFromElement();
+  atm.SetCharge( charge );
+  Residue res( unitName, resx, ' ', ' ' );
+  topOut.AddTopAtom( atm, res );
+  return 0;
+}
+
+/** Read positions line. */
+int DataIO_AmberLib::read_positions(std::vector<Vec3>& positions, std::string const& line)
+{
+  double x, y, z;
+  if (sscanf(line.c_str(), "%lf %lf %lf", &x, &y, &z) != 3) {
+    mprinterr("Error: Expected 3 columns for positions line: %s\n", line.c_str());
+    return 1;
+  }
+  positions.push_back( Vec3(x, y, z) );
+  return 0;
+}
+
+/** Read bonds line */
+int DataIO_AmberLib::read_bonds(Topology& topOut, std::string const& line) {
+  int at0, at1, flags;
+  if (sscanf(line.c_str(), "%i %i %i", &at0, &at1, &flags) != 3) {
+    mprinterr("Error: Expected 3 columns for connectivity line: %s\n", line.c_str());
+    return 1;
+  }
+  topOut.AddBond( at0-1, at1-1 );
+  return 0;
+}
+
+/** Read connections line */
+int DataIO_AmberLib::read_connect(AssociatedData_Connect& ConnectAtoms, std::string const& line) {
+  int connectAtom = -1;
+  if (sscanf(line.c_str(), "%i", &connectAtom) != 1) {
+    mprinterr("Error: Expected 1 column for connect line: %s\n", line.c_str());
+    return 1;
+  }
+  // Amber lib atoms start from 1
+  if (connectAtom < 1) {
+    mprintf("Warning: Atom index < 1 in connect line: %s\n", line.c_str());
+  }
+  ConnectAtoms.AddConnectAtom( connectAtom-1 );
+  return 0;
+}
+
+/** Read a unit from OFF file. It is expected that the next line from
+  * infile is the first entry in the unit.atoms table.
+  */
+int DataIO_AmberLib::read_unit(DataSet_Coords* crd,
+                               BufferedLine& infile, std::string& Line,
+                               std::string const& unitName)
+const
+{
+  AssociatedData_Connect ConnectAtoms;
+  SectionType currentSection = id_section( Line, unitName );
+  if (currentSection == UNKNOWN_SECTION) {
+    mprinterr("Error: Could not ID first section: %s\n", Line.c_str());
+    return 1;
+  }
+  if (debug_ > 1) mprintf("DEBUG: First section is %s\n", sectionStr_[currentSection]);
+
+  Topology top;
+  top.SetParmName( unitName, FileName() );
+  std::vector<Vec3> positions;
+  Frame frm;
+
+  bool readUnit = true;
+  while (readUnit) {
+    const char* lineptr = infile.Line();
+    if (lineptr == 0) {
+      readUnit = false;
+      break;
+    }
+    Line.assign(lineptr);
+    if (!Line.empty()) {
+      if (debug_ > 2) mprintf("DEBUG: Line: %s\n", Line.c_str());
+      //ArgList cols( Line, " \t\n" );
+      if (Line[0] == '!') {
+        // See if we are at another unit
+        ArgList tmparg( Line, ". " );
+        if (tmparg[2] == "unit" && tmparg[3] == "atoms" && tmparg[4] == "table") {
+          readUnit = false;
+          break;
+        }
+        currentSection = id_section( Line, unitName );
+        if (currentSection == UNKNOWN_SECTION) {
+          mprintf("Warning: Could not ID section: %s\n", Line.c_str());
+        } else {
+          if (debug_ > 1) mprintf("DEBUG: Section is %s\n", sectionStr_[currentSection]);
+        }
+      } else if (currentSection == ATOMTABLE) {
+        if (read_atoms(top, Line, unitName)) return 1;
+      } else if (currentSection == CONNECTIVITY) {
+        if (read_bonds(top, Line)) return 1;
+      } else if (currentSection == POSITIONS) {
+        if (read_positions(positions, Line)) return 1;
+      } else if (currentSection == CONNECT) {
+        if (read_connect(ConnectAtoms, Line)) return 1;
+      }
+    }
+  }
+  top.CommonSetup();
+  if (debug_ > 1) top.Summary();
+  frm.SetupFrameV( top.Atoms(), CoordinateInfo() );
+  frm.ClearAtoms();
+  for (std::vector<Vec3>::const_iterator it = positions.begin(); it != positions.end(); ++it)
+    frm.AddVec3( *it );
+
+  crd->CoordsSetup(top, frm.CoordsInfo());
+  crd->AddFrame( frm );
+  crd->AssociateData( &ConnectAtoms );
+  if (debug_ > 1) ConnectAtoms.Ainfo();
+  mprintf("\n");
+  
+  return 0;
+}
+
+// DataIO_AmberLib::WriteHelp()
+void DataIO_AmberLib::WriteHelp()
+{
+
+}
+
+// DataIO_AmberLib::processWriteArgs()
+int DataIO_AmberLib::processWriteArgs(ArgList& argIn)
+{
+
+  return 0;
+}
+
+// DataIO_AmberLib::WriteData()
+int DataIO_AmberLib::WriteData(FileName const& fname, DataSetList const& dsl)
+{
+
+  return 1;
+}
diff --git a/src/DataIO_AmberLib.h b/src/DataIO_AmberLib.h
new file mode 100644
index 0000000000..9f8952fa37
--- /dev/null
+++ b/src/DataIO_AmberLib.h
@@ -0,0 +1,36 @@
+#ifndef INC_DATAIO_AMBERLIB_H
+#define INC_DATAIO_AMBERLIB_H
+#include "DataIO.h"
+class BufferedLine;
+class AssociatedData_Connect;
+/// <Enter description of DataIO_AmberLib here>
+class DataIO_AmberLib : public DataIO {
+  public:
+    DataIO_AmberLib();
+    static void ReadHelp();
+    static void WriteHelp();
+    static BaseIOtype* Alloc() { return (BaseIOtype*)new DataIO_AmberLib(); }
+    int processReadArgs(ArgList&);
+    int ReadData(FileName const&, DataSetList&, std::string const&);
+    int processWriteArgs(ArgList&);
+    int WriteData(FileName const&, DataSetList const&);
+    bool ID_DataFormat(CpptrajFile&);
+  private:
+    // Keep in sync with sectionStr_
+    enum SectionType { ATOMTABLE = 0, PERTINFO, BOUNDBOX, CHILDSEQUENCE, CONNECT,
+                       CONNECTIVITY, HIERARCHY, UNITNAME, POSITIONS, RESCONNECT,
+                       RESIDUES, SOLVENTCAP, VELOCITIES, UNKNOWN_SECTION };
+    /// Strings corresponding to section type
+    static const char* sectionStr_[];
+
+    /// ID OFF section from line
+    static inline SectionType id_section(std::string const&, std::string const&);
+    /// Read unit from OFF file
+    int read_unit(DataSet_Coords*, BufferedLine&, std::string&, std::string const&) const;
+
+    static int read_atoms(Topology&, std::string const&, std::string const&);
+    static int read_bonds(Topology&, std::string const&);
+    static int read_positions(std::vector<Vec3>&, std::string const&);
+    static int read_connect(AssociatedData_Connect&, std::string const&);
+};
+#endif
diff --git a/src/DataIO_AmberPrep.cpp b/src/DataIO_AmberPrep.cpp
new file mode 100644
index 0000000000..1424ec29cd
--- /dev/null
+++ b/src/DataIO_AmberPrep.cpp
@@ -0,0 +1,421 @@
+#include "DataIO_AmberPrep.h"
+#include "CpptrajStdio.h"
+#include "BondSearch.h"
+#include "BufferedLine.h"
+#include "DataSet_Coords.h"
+#include "StringRoutines.h"
+#include "Structure/Zmatrix.h"
+
+/// CONSTRUCTOR
+DataIO_AmberPrep::DataIO_AmberPrep() :
+  removeDummyAtoms_(true)
+{ }
+
+// DataIO_AmberPrep::ID_DataFormat()
+bool DataIO_AmberPrep::ID_DataFormat(CpptrajFile& infile)
+{
+
+  return false;
+}
+
+// DataIO_AmberPrep::ReadHelp()
+void DataIO_AmberPrep::ReadHelp()
+{
+  mprintf("\tkeepdummyatoms : Keep dummy atoms instead of removing them.\n");
+}
+
+// DataIO_AmberPrep::processReadArgs()
+int DataIO_AmberPrep::processReadArgs(ArgList& argIn)
+{
+  removeDummyAtoms_ = !argIn.hasKey("keepdummyatoms");
+  return 0;
+}
+
+/// Used to check for premature EOF
+static inline int CheckLine(const char* line) {
+  if (line==0) {
+    mprinterr("Error: Unexpected end of prep file.\n");
+    return 1;
+  }
+  return 0;
+}
+
+/** Read CHARGE section. */
+int DataIO_AmberPrep::readCHARGE(BufferedLine& infile) const {
+  const char* line = infile.Line();
+  while (line != 0 && line[0] != '\0') {
+    if (debug_ > 0) mprintf("DEBUG: CHARGE: %s\n", line);
+    line = infile.Line();
+  }
+  return 0;
+}
+
+/** Read LOOP section. */
+int DataIO_AmberPrep::readLOOP(BufferedLine& infile, AtPairArray& BondPairs) const {
+  const char* line = infile.Line();
+  while (line != 0 && line[0] != '\0') {
+    if (debug_ > 0) mprintf("DEBUG: LOOP: %s\n", line);
+    ArgList atpair(line, " \t");
+    if (atpair.Nargs() != 2) {
+      mprinterr("Error: Expected 2 atom names, got %i: %s\n", atpair.Nargs(), line);
+      return 1;
+    }
+    BondPairs.push_back(AtPairType(atpair[0], atpair[1]));
+    line = infile.Line();
+  }
+  return 0;
+}
+
+/** Read IMPROPER section. */
+int DataIO_AmberPrep::readIMPROPER(BufferedLine& infile) const {
+  const char* line = infile.Line();
+  while (line != 0 && line[0] != '\0') {
+    if (debug_ > 0) mprintf("DEBUG: IMPROPER: %s\n", line);
+    line = infile.Line();
+  }
+  return 0;
+}
+
+/** Read 1 or more PREP residue sections (cards 3-10).
+  * \return 1 if error, -1 if STOP/EOF, 0 if more residues to be read.
+  */
+int DataIO_AmberPrep::readAmberPrep(BufferedLine& infile, DataSetList& dsl, std::string const& dsname)
+const
+{
+  // 3 - Title
+  // Descriptive header for the residue
+  const char* line = infile.Line();
+  // If EOF here, assume missing STOP
+  if (line == 0) {
+    mprintf("Warning: Prep file '%s' missing STOP.\n", infile.Filename().base());
+    return -1;
+  }
+  // Check for STOP
+  if (std::string(line) == "STOP")
+    return -1;
+  if (debug_ > 0)
+    mprintf("DEBUG: Prep title: '%s'\n", line);
+
+  // 4 - Name of output file if an individual res file is being generated
+  // NAMF
+  // Format (A80)
+  line = infile.Line();
+  if (CheckLine(line)) return 1;
+  // 5 - NAMRES, INTX, KFORM
+  // NAMERES - a unique name for the residue 
+  // INTX - Flag for the type of coords to be saved for LINK module. INT - internal, XYZ - cart.
+  // KFORM - Format of output for individual residue files 0 - formatted, 1 - binary
+  // FORMAT (2A, I)
+  line = infile.Line();
+  if (CheckLine(line)) return 1;
+  ArgList args( line );
+  if (args.Nargs() != 3) {
+    mprinterr("Error: Expected NAMRES, INTX, KFORM: %s\n", line);
+    return 1;
+  }
+  std::string resName = args.GetStringNext();
+  std::string coordFlag = args.GetStringNext();
+  int kform = args.getNextInteger(-1);
+  if (debug_ > 0)
+    mprintf("DEBUG: %s %s %i\n", resName.c_str(), coordFlag.c_str(), kform);
+  // 6 - IFIXC , IOMIT , ISYMDU , IPOS
+  // FORMAT (4A)
+  // IFIXC      Flag for the type of input geometry of the residue(s)
+  //    'CORRECT' The geometry is input as internal coordinates with
+  //              correct order according to the tree structure.
+  //              NOTE: the tree structure types ('M', 'S', etc) and order
+  //              must be defined correctly: NA(I), NB(I), and NC(I) on card
+  //              8 are always ignored.
+  //    'CHANGE'  It is input as cartesian coordinates or part cartesian
+  //              and part internal.  Cartesians should precede internals
+  //              to ensure that the resulting coordinates are correct.
+  //              Coordinates need not be in correct order, since each
+  //              is labeled with its atom number. NOTE: NA(I), NB(I), and
+  //              NC(I) on card 8 must be omitted for cartesian coordinates
+  //              with this option.
+  //
+  // IOMIT      Flag for the omission of dummy atoms
+  //    'OMIT'    dummy atoms will be deleted after generating all the
+  //              information (this is used for all but the first residue
+  //              in the system)
+  //    'NOMIT'   they will not be deleted (dummy atoms are retained for
+  //              the first residue of the system.  others are omitted)
+  //
+  // ISYMDU     Symbol for the dummy atoms.  The symbol must be
+  //            be unique.  It is preferable to use 'DU' for it.
+  //
+  // IPOS       Flag for the position of dummy atoms to be deleted
+  //    'ALL'     all the dummy atoms will be deleted
+  //    'BEG'     only the beginning dummy atoms will be deleted
+  line = infile.Line();
+  if (CheckLine(line)) return 1;
+  args.SetList( line, " \t" );
+  if (args.Nargs() != 4) {
+    mprinterr("Error: Expected IFIXC, IOMIT, ISYMDU, IPOS: %s\n", line);
+    return 1;
+  }
+  std::string IFIXC  = args.GetStringNext();
+  std::string IOMIT  = args.GetStringNext();
+  std::string ISYMDU = args.GetStringNext();
+  std::string IPOS   = args.GetStringNext();
+  if (debug_ > 0)
+    mprintf("DEBUG: %s %s %s %s\n", IFIXC.c_str(), IOMIT.c_str(), ISYMDU.c_str(), IPOS.c_str());
+  if (IFIXC != "CORRECT") {
+    mprinterr("Error: IFIXC is not 'CORRECT' (%s=); only internal coordinates currently supported.\n",
+              IFIXC.c_str());
+    return 1;
+  }
+  // 7 - CUT
+  // The cutoff distance for loop closing bonds which
+  // cannot be defined by the tree structure.  Any pair of
+  // atoms within this distance is assumed to be bonded.
+  // TODO implement bond search
+  line = infile.Line();
+  if (CheckLine(line)) return 1;
+  double bondCutoff = 0;
+  if (line[0] != '\0')
+    bondCutoff = convertToDouble( std::string(line) );
+  if (bondCutoff > 0.0)
+    mprintf("Warning: Non-zero cutoff in prep file (%g); will search for additional\n"
+            "Warning:  bonds based on distances.\n", bondCutoff);
+  //     0 1         2         3        4     5     6     7    8        9      10
+  // 8 - I IGRAPH(I) ISYMBL(I) ITREE(I) NA(I) NB(I) NC(I) R(I) THETA(I) PHI(I) CHG(I) [I = 1, NATOM]
+  // FORMAT(I,3A,3I,4F)
+  // Terminated by a blank line
+  using namespace Cpptraj::Structure;
+  Zmatrix zmatrix;
+  zmatrix.SetDebug( debug_ );
+  // Topology
+  //DataSet* ds = dsl.AddSet( DataSet::TOPOLOGY, MetaData(dsname, "top") );
+  //if (ds == 0) {
+  //  mprinterr("Error: Could not create topology for prep.\n");
+  //  return 1;
+  //}
+  //Topology& top = ((DataSet_Topology*)ds)->ModifyTop();
+  Topology top;
+  top.SetParmName( resName, infile.Filename() );
+  // Residue
+  Residue res(resName, 1, ' ', ' ');
+  // Loop over entries
+  line = infile.Line();
+  if (CheckLine(line)) return 1;
+  int atIdx = 0;
+  while (line[0] != '\0') {
+    if (debug_ > 1)
+      mprintf("DEBUG: '%s'\n", line);
+    args.SetList( line, " \t" );
+    if (args.Nargs() != 11) {
+      mprinterr("Error: Expected 11 columns in prep line, got %i\n", args.Nargs());
+      return 1;
+    }
+    double charge = convertToDouble(args[10]);
+    // Add top atom
+    if (args[2] == "EP") {
+      // Special case for extra points
+      Atom atm(args[1], "XP");
+      atm.SetTypeName(args[2]);
+      atm.SetCharge(charge);
+      top.AddTopAtom(atm, res);
+    } else
+      top.AddTopAtom( Atom(args[1], args[2], charge), res );
+    // Add zmatrix entry. In prep file, indices start from 1.
+    int atI = convertToInteger(args[0]) - 1;
+    if (atI != atIdx) {
+      mprinterr("Error: Expected index %i, got %i\n", atIdx + 1, atI + 1);
+      return 1;
+    }
+    int atJ = convertToInteger(args[4]) - 1;
+    int atK = convertToInteger(args[5]) - 1;
+    int atL = convertToInteger(args[6]) - 1;
+    double dist  = convertToDouble(args[7]);
+    double theta = convertToDouble(args[8]);
+    double phi   = convertToDouble(args[9]);
+    //if (args[2] == ISYMDU) {
+      if (zmatrix.AddIC( InternalCoords(atIdx, atJ, atK, atL, dist, theta, phi) ))
+        return 1;
+    //} else
+    //  zmatrix.AddIC( InternalCoords(atIdx, atJ, atK, atL, dist, theta, phi) );
+    atIdx++;
+    line = infile.Line();
+    if (line == 0) break;
+  }
+  // 9 - Read additional information about the residue.
+  // CHARGE - Read additional partial atomic charges. FORMAT (5f)
+  // LOOP - Read explicit loop closing bonds
+  // IMPROPER - Read improper torsion angles. 
+  AtPairArray BondPairs;
+  while (line != 0) {
+    if (line[0] != '\0') {
+      std::string lineStr(line);
+      if (lineStr == "DONE") {
+
+        break;
+      } else if (lineStr == "CHARGE") {
+        readCHARGE(infile);
+      } else if (lineStr == "LOOP") {
+        if (readLOOP(infile, BondPairs)) {
+          mprinterr("Error: Reading LOOP section.\n");
+          return 1;
+        }
+      } else if (lineStr == "IMPROPER") {
+        readIMPROPER(infile);
+      } 
+    }
+    line = infile.Line();
+  }
+  // -----------------------------------
+  // Add bonds to topology
+  for (Zmatrix::const_iterator it = zmatrix.begin(); it != zmatrix.end(); ++it)
+    if (it->AtJ() != InternalCoords::NO_ATOM)
+      top.AddBond( it - zmatrix.begin(), it->AtJ() );
+  for (AtPairArray::const_iterator it = BondPairs.begin(); it != BondPairs.end(); ++it) {
+    int idx1 = top.FindAtomInResidue(0, it->first);
+    if (idx1 < 0) {
+      mprinterr("Error: Could not find LOOP atom '%s'\n", it->first.c_str());
+      return 1;
+    }
+    int idx2 = top.FindAtomInResidue(0, it->second);
+    if (idx2 < 0) {
+      mprinterr("Error: Could not find LOOP atom '%s'\n", it->second.c_str());
+      return 1;
+    }
+    top.AddBond( idx1, idx2 );
+  }
+  // Frame
+  Frame frm( top.Natom() );
+  // Internal coords to cart
+  if (zmatrix.SetToFrame( frm )) {
+    mprinterr("Error: IC to Cartesian coords failed.\n");
+    return 1;
+  }
+  // Bond search
+  if (bondCutoff > 0) {
+    BondSearch bondSearch;
+    bondSearch.FindBonds( top, BondSearch::SEARCH_REGULAR, frm, 0.2, debug_ );
+  }
+  // Set up topology
+  top.CommonSetup(true, false);
+  if (debug_ > 0)
+    top.Summary();
+  if (debug_ > 1)
+    zmatrix.print();
+  // Create COORDS set
+  //ds = dsl.AddSet( DataSet::REF_FRAME, MetaData(dsname, "crd") );
+  DataSet* ds = dsl.AddSet( DataSet::REF_FRAME, MetaData(dsname, resName) );
+  if (ds == 0) {
+    mprinterr("Error: Could not create coordinates for prep.\n");
+    return 1;
+  }
+  DataSet_Coords* CRD = static_cast<DataSet_Coords*>( ds );
+  
+  // Delete dummy atoms if needed
+  if (removeDummyAtoms_) {
+    AtomMask keepAtoms;
+    if (keepAtoms.SetMaskString( "!@%" + ISYMDU )) {
+      mprinterr("Error: Could not set up mask string to remove dummy atoms.\n");
+      return 1;
+    }
+    if (top.SetupIntegerMask( keepAtoms )) {
+      mprinterr("Error: Could not set up mask '%s' to remove dummy atoms.\n", keepAtoms.MaskString());
+      return 1;
+    }
+    if (debug_ > 0) keepAtoms.MaskInfo();
+    if (keepAtoms.Nselected() == top.Natom()) {
+      mprintf("\tNo dummy atoms to remove.\n");
+    } else {
+      Topology* newTop = top.modifyStateByMask( keepAtoms );
+      if (newTop == 0) {
+        mprinterr("Error: Could not remove dummy atoms.\n");
+        return 1;
+      }
+      Frame newFrame( frm, keepAtoms );
+      top = *newTop;
+      delete newTop;
+      frm = newFrame;
+      if (debug_ > 0) top.Summary();
+    }
+  }
+  // DEBUG - back convert
+/*  mprintf("DEBUG: BACK CONVERT %s\n", resName.c_str());
+  mprinterr("DEBUG: BACK CONVERT %s\n", resName.c_str());
+  Zmatrix tempZ;
+  tempZ.SetDebug(10);
+  //tempZ.SetSeedPositions(frm, top, 5, 0, 1);
+  int tempErr = tempZ.SetFromFrame( frm, top, 0 );
+  if (tempErr != 0) {
+    mprintf("DEBUG Error: Back converting %s\n", resName.c_str());
+    mprinterr("DEBUG Error: Back converting %s\n", resName.c_str());
+    return 1;
+  }
+  tempZ.print();
+  Frame tmpFrame(top.Natom());
+  if (tempErr == 0) {
+    tempZ.SetToFrame(tmpFrame);
+    for (int ii = 0; ii < tmpFrame.Natom(); ii++)
+      tmpFrame.printAtomCoord(ii);
+  }*/
+  // Output Set up frame set
+  if (CRD->CoordsSetup(top, CoordinateInfo())) {
+    mprinterr("Error: Could not set up COORDS set for prep.\n");
+    return 1;
+  }
+  CRD->SetCRD(0, frm);
+
+  return 0;
+}
+
+// DataIO_AmberPrep::ReadData()
+int DataIO_AmberPrep::ReadData(FileName const& fname, DataSetList& dsl, std::string const& dsname)
+{
+  BufferedLine infile;
+
+  if (infile.OpenFileRead(fname)) {
+    mprinterr("Error: Could not open '%s'\n", fname.full());
+    return 1;
+  }
+  // 1 - Control for data base generation
+  // IDBGEN, IREST, ITYPF
+  // Format (3I)
+  const char* line = infile.Line();
+  if (CheckLine(line)) return 1;
+  // 2 - Name of the data base file. Blank if not data base gen.
+  // NAMDBF
+  // Format (A80)
+  line = infile.Line();
+  if (CheckLine(line)) return 1;
+
+  bool readPrep = true;
+  while (readPrep) {
+    int errStat = readAmberPrep(infile, dsl, dsname);
+    if (errStat == 1) {
+      mprinterr("Error: Could not read residue(s) from prep file.\n");
+      return 1;
+    } else if (errStat == -1) {
+      readPrep = false;
+    }
+  }
+
+  infile.CloseFile();
+
+  return 0;
+}
+
+// DataIO_AmberPrep::WriteHelp()
+void DataIO_AmberPrep::WriteHelp()
+{
+
+}
+
+// DataIO_AmberPrep::processWriteArgs()
+int DataIO_AmberPrep::processWriteArgs(ArgList& argIn)
+{
+
+  return 0;
+}
+
+// DataIO_AmberPrep::WriteData()
+int DataIO_AmberPrep::WriteData(FileName const& fname, DataSetList const& dsl)
+{
+
+  return 1;
+}
diff --git a/src/DataIO_AmberPrep.h b/src/DataIO_AmberPrep.h
new file mode 100644
index 0000000000..2f86f4adab
--- /dev/null
+++ b/src/DataIO_AmberPrep.h
@@ -0,0 +1,30 @@
+#ifndef INC_DATAIO_AMBERPREP_H
+#define INC_DATAIO_AMBERPREP_H
+#include <utility>
+#include <vector>
+#include "DataIO.h"
+class BufferedLine;
+/// Read in the Amber prep file format 
+class DataIO_AmberPrep : public DataIO {
+  public:
+    DataIO_AmberPrep();
+    static void ReadHelp();
+    static void WriteHelp();
+    static BaseIOtype* Alloc() { return (BaseIOtype*)new DataIO_AmberPrep(); }
+    int processReadArgs(ArgList&);
+    int ReadData(FileName const&, DataSetList&, std::string const&);
+    int processWriteArgs(ArgList&);
+    int WriteData(FileName const&, DataSetList const&);
+    bool ID_DataFormat(CpptrajFile&);
+  private:
+    typedef std::pair<std::string, std::string> AtPairType;
+    typedef std::vector<AtPairType> AtPairArray;
+
+    int readCHARGE(BufferedLine&) const;
+    int readLOOP(BufferedLine&, AtPairArray&) const;
+    int readIMPROPER(BufferedLine&) const;
+    int readAmberPrep(BufferedLine&, DataSetList&, std::string const&) const;
+
+    bool removeDummyAtoms_; ///< Remove dummy atoms if true
+};
+#endif
diff --git a/src/DataSet.cpp b/src/DataSet.cpp
index 5135067fd1..b9e0d5b797 100644
--- a/src/DataSet.cpp
+++ b/src/DataSet.cpp
@@ -32,6 +32,7 @@ const char* DataSet::Descriptions_[] = {
   "vector with scalar",         // VECTOR_SCALAR
   "unsigned integer",           // UNSIGNED_INTEGER
   "frames",                     // FRAMES
+  "zmatrix",                    // ZMATRIX
   "unknown"                     // UNKNOWN_DATA
 };
 
diff --git a/src/DataSet.h b/src/DataSet.h
index 98868cef3c..f619652f4d 100644
--- a/src/DataSet.h
+++ b/src/DataSet.h
@@ -29,7 +29,7 @@ class DataSet {
       COORDS, VECTOR, MODES, GRID_FLT, GRID_DBL, REMLOG, XYMESH, TRAJ, REF_FRAME,
       MAT3X3, TOPOLOGY, PH, PH_EXPL, PH_IMPL,
       PARAMETERS, PMATRIX_MEM, PMATRIX_NC, TENSOR, STRINGVAR, VECTOR_SCALAR, UNSIGNED_INTEGER,
-      FRAMES,
+      FRAMES, ZMATRIX,
       UNKNOWN_DATA
     };
     /// Group DataSet belongs to.
@@ -85,7 +85,7 @@ class DataSet {
 #   endif
     // -----------------------------------------------------
     /// Associate additional data with this set.
-    void AssociateData(AssociatedData* a) { associatedData_.push_back( a->Copy() ); }
+    void AssociateData(AssociatedData const* a) { associatedData_.push_back( a->Copy() ); }
     /// Set DataSet MetaData
     int SetMeta(MetaData const&);
     /// Set DataSet ensemble number.
diff --git a/src/DataSetList.cpp b/src/DataSetList.cpp
index 332f90c7a9..a6662da59e 100644
--- a/src/DataSetList.cpp
+++ b/src/DataSetList.cpp
@@ -35,6 +35,7 @@
 #include "DataSet_Vector_Scalar.h"
 #include "DataSet_unsignedInt.h"
 #include "DataSet_Coords_FRM.h"
+#include "DataSet_Zmatrix.h"
 
 bool DataSetList::useDiskCache_ = false;
 
@@ -93,6 +94,7 @@ DataSet* DataSetList::NewSet(DataSet::DataType typeIn) {
     case DataSet::TENSOR        : ds = DataSet_Tensor::Alloc(); break;
     case DataSet::STRINGVAR     : ds = DataSet_StringVar::Alloc(); break;
     case DataSet::VECTOR_SCALAR : ds = DataSet_Vector_Scalar::Alloc(); break;
+    case DataSet::ZMATRIX       : ds = DataSet_Zmatrix::Alloc(); break;
     // Sanity check
     default:
       mprinterr("Internal Error: No allocator for DataSet type '%s'\n",
diff --git a/src/DataSet_Coords_REF.cpp b/src/DataSet_Coords_REF.cpp
index 1fcdce3cce..10abce711f 100644
--- a/src/DataSet_Coords_REF.cpp
+++ b/src/DataSet_Coords_REF.cpp
@@ -33,8 +33,7 @@ void DataSet_Coords_REF::AddFrame(Frame const& fIn) {
 
 /** Set REF from incoming frame. */
 void DataSet_Coords_REF::SetCRD(int idx, Frame const& fIn) {
-  // TODO warn if idx not zero?
-  if (idx == 0)
+  if (idx != 0)
     mprintf("Warning: In reference set '%s', attempting to set index which is not 1 (%i)\n", legend(), idx+1);
   if (frame_.empty())
     frame_.SetupFrame( fIn );
diff --git a/src/DataSet_Topology.h b/src/DataSet_Topology.h
index fcdbef4e55..e9328469c4 100644
--- a/src/DataSet_Topology.h
+++ b/src/DataSet_Topology.h
@@ -2,6 +2,7 @@
 #define INC_DATASET_TOPOLOGY
 #include "DataSet.h"
 #include "Topology.h"
+class ArgList;
 /// Hold Topology data
 class DataSet_Topology : public DataSet {
   public:
@@ -22,6 +23,7 @@ class DataSet_Topology : public DataSet {
     int LoadTopFromFile(ArgList const&, int);
     int StripTop( std::string const& );
     void SetTop(Topology const& t) { top_ = t;            }
+    Topology& ModifyTop() { return top_; }
     void SetPindex(int p)          { top_.SetPindex( p ); }
     Topology* TopPtr()             { return &top_; } // NOTE: pytraj currently relies on this 
     Topology const& Top() const    { return top_;  }
diff --git a/src/DataSet_Zmatrix.cpp b/src/DataSet_Zmatrix.cpp
new file mode 100644
index 0000000000..2ea9d8ae29
--- /dev/null
+++ b/src/DataSet_Zmatrix.cpp
@@ -0,0 +1,49 @@
+#include "DataSet_Zmatrix.h"
+#include "CpptrajStdio.h"
+#include "Structure/Zmatrix.h"
+
+using namespace Cpptraj::Structure;
+
+/** CONSTRUCTOR */
+DataSet_Zmatrix::DataSet_Zmatrix() :
+  DataSet(ZMATRIX, GENERIC, TextFormat(TextFormat::DOUBLE, 8, 3, 7), 1), // i j k l dist theta phi
+  zmatrix_(0)
+{
+  zmatrix_ = new Zmatrix();
+}
+
+/** DESTRUCTOR */
+DataSet_Zmatrix::~DataSet_Zmatrix() {
+  if (zmatrix_ != 0) delete zmatrix_;
+}
+
+/** \return memory usage in bytes. */
+size_t DataSet_Zmatrix::MemUsageInBytes() const {
+  return zmatrix_->sizeInBytes();
+}
+
+/** \return number of internal coords */
+size_t DataSet_Zmatrix::Size() const {
+  return zmatrix_->N_IC();
+}
+
+/** Reserve space in the IC_ array. */
+int DataSet_Zmatrix::Allocate( SizeArray const& sizeIn ) {
+  if (!sizeIn.empty())
+    zmatrix_->reserve( sizeIn[0] );
+  return 0;
+}
+
+/** Write to file. */
+void DataSet_Zmatrix::WriteBuffer(CpptrajFile &cbuffer, SizeArray const& frame) const {
+  if (frame[0] >= zmatrix_->N_IC())
+    cbuffer.Printf(format_.fmt(), 0, 0, 0, 0, 0, 0, 0);
+  else {
+    //mprintf("DEBUG: Format: %s\n", format_.fmt());
+    InternalCoords const& ic = (*zmatrix_)[frame[0]];
+    cbuffer.Printf(format_.fmt(),
+                   (double)(ic.AtI()+1), (double)(ic.AtJ()+1),
+                   (double)(ic.AtK()+1), (double)(ic.AtL()+1),
+                   ic.Dist(), ic.Theta(), ic.Phi());
+  }
+}
diff --git a/src/DataSet_Zmatrix.h b/src/DataSet_Zmatrix.h
new file mode 100644
index 0000000000..6e667b3c16
--- /dev/null
+++ b/src/DataSet_Zmatrix.h
@@ -0,0 +1,31 @@
+#ifndef INC_DATASET_ZMATRIX_H
+#define INC_DATASET_ZMATRIX_H
+#include "DataSet.h"
+namespace Cpptraj {
+namespace Structure {
+class Zmatrix;
+}
+}
+/// Hold a Z matrix 
+class DataSet_Zmatrix : public DataSet {
+  public:
+    DataSet_Zmatrix();
+    ~DataSet_Zmatrix();
+    static DataSet* Alloc() { return (DataSet*)new DataSet_Zmatrix(); }
+    // ----- DataSet functions -------------------
+    size_t Size() const;
+    int Allocate(SizeArray const&);
+    void WriteBuffer(CpptrajFile&, SizeArray const&) const;
+    size_t MemUsageInBytes() const;
+    void Info()                                      const { return; }
+    void Add(size_t, const void*)                          { return; }
+    int Append(DataSet*)                                   { return 1; }
+#   ifdef MPI
+    int Sync(size_t, std::vector<int> const&, Parallel::Comm const&) { return 1; }
+#   endif
+    // -------------------------------------------
+    Cpptraj::Structure::Zmatrix* Zptr() const { return zmatrix_; }
+  private:
+    Cpptraj::Structure::Zmatrix* zmatrix_;
+};
+#endif
diff --git a/src/Exec_DataSetCmd.cpp b/src/Exec_DataSetCmd.cpp
index 28d559b36b..9d60c346f8 100644
--- a/src/Exec_DataSetCmd.cpp
+++ b/src/Exec_DataSetCmd.cpp
@@ -8,11 +8,13 @@
 #include "DataSet_Mesh.h"
 #include "DataSet_Mat3x3.h"
 #include "StringRoutines.h"
+#include "AssociatedData_NOE.h"
+#include "AssociatedData_Connect.h"
 
 // Exec_DataSetCmd::Help()
 void Exec_DataSetCmd::Help() const {
   mprintf("\t{legend|makexy|vectorcoord|cat|make2d|droppoints|keeppoints|remove|\n"
-          "\t dim|outformat|invert|shift|mode|type} <options>\n");
+          "\t connect|dim|outformat|invert|shift|mode|type} <options>\n");
   mprintf("  Type 'help dataset <cmd>' for detailed subcommand help.\n");
 }
 
@@ -56,6 +58,9 @@ void Exec_DataSetCmd::Help(ArgList& argIn) const {
     Help_InvertSets();
   } else if (argIn.hasKey("shift")) {
     Help_Shift();
+  } else if (argIn.hasKey("connect")) {
+    mprintf("  connect {%s | [headmask <headmask>] [tailmask <tailmask>]}\n",
+            AssociatedData_Connect::HelpText);
   } else if (argIn.hasKey("mode")) {
     mprintf("  [mode <mode>] [type <type>] <set arg1> [<set arg 2> ...]\n");
     mprintf("      <mode>: ");
@@ -96,6 +101,9 @@ Exec::RetType Exec_DataSetCmd::Execute(CpptrajState& State, ArgList& argIn) {
   } else if (argIn.hasKey("make2d")) {      // Create 2D matrix from 1D set
     err = Make2D(State, argIn);
   // ---------------------------------------------
+  } else if (argIn.hasKey("connect")) {     // Add connection atoms to COORDS set
+    err = SetConnect(State, argIn);
+  // ---------------------------------------------
   } else if (argIn.hasKey("vectorcoord")) { // Extract vector X/Y/Z coord as new set
     err = VectorCoord(State, argIn);
   // ---------------------------------------------
@@ -296,6 +304,102 @@ Exec::RetType Exec_DataSetCmd::ModifyPoints(CpptrajState& State, ArgList& argIn,
   return CpptrajState::OK;
 }
 
+/// Function to select a single atom from a Topology based on mask expression
+static inline int select_atom(std::string const& maskexpr, Topology const& topIn)
+{
+  AtomMask mask;
+  if (mask.SetMaskString( maskexpr )) {
+    mprinterr("Error: Invalid mask expression: %s\n", maskexpr.c_str());
+    return -2;
+  }
+  if (topIn.SetupIntegerMask( mask )) {
+    mprinterr("Error: Could not set up mask %s\n", mask.MaskString());
+    return -2;
+  }
+  if (mask.None()) {
+    mprintf("Warning: Mask %s selects no atoms for %s\n", mask.MaskString(), topIn.c_str());
+    return -1;
+  }
+  if (mask.Nselected() > 1) {
+    mprinterr("Error: Mask %s selects more than 1 atom for %s\n", mask.MaskString(), topIn.c_str());
+    return -2;
+  }
+  return mask[0];
+}
+
+// Exec_DataSetCmd::SetConnect()
+Exec::RetType Exec_DataSetCmd::SetConnect(CpptrajState& State, ArgList& argIn) {
+  // Keywords
+  AssociatedData_Connect connect;
+  std::string headmaskstr = argIn.GetStringKey("headmask");
+  std::string tailmaskstr = argIn.GetStringKey("tailmask");
+  bool use_mask = true;
+  if (headmaskstr.empty() && tailmaskstr.empty()) {
+    use_mask = false;
+    if (connect.ProcessAdataArgs(argIn)) {
+      mprinterr("Error: Could not process 'connect' keywords.\n");
+      return CpptrajState::ERR;
+    }
+    mprintf("\t");
+    connect.Ainfo();
+    mprintf("\n");
+  } else {
+    if (!headmaskstr.empty()) mprintf("\tHead atom mask: %s\n", headmaskstr.c_str());
+    if (!tailmaskstr.empty()) mprintf("\tTail atom mask: %s\n", tailmaskstr.c_str());
+  }
+  // Get Data set(s)
+  typedef std::vector<DataSet_Coords*> DCarray;
+  DCarray inputSets;
+  std::string crdsetarg = argIn.GetStringNext();
+  if (crdsetarg.empty())
+    mprintf("Warning: No data set arguments specified.\n");
+  while (!crdsetarg.empty()) {
+    DataSetList dsl1 = State.DSL().GetMultipleSets( crdsetarg );
+    for (DataSetList::const_iterator it = dsl1.begin(); it != dsl1.end(); ++it)
+    {
+      if ( (*it)->Group() != DataSet::COORDINATES ) {
+        mprintf("Warning: 'connect' only works with COORDS sets; '%s' is not COORDS.\n", (*it)->legend());
+      } else {
+        inputSets.push_back( static_cast<DataSet_Coords*>( *it ) );
+      }
+    }
+    crdsetarg = argIn.GetStringNext();
+  }
+  if (inputSets.empty()) {
+    mprinterr("Error: 'connect': No data sets selected.\n");
+    return CpptrajState::ERR;
+  }
+  mprintf("\t%zu sets.\n", inputSets.size());
+  for (DCarray::const_iterator it = inputSets.begin(); it != inputSets.end(); ++it) {
+    // Process mask if needed
+    if (use_mask) {
+      int head = -1;
+      if (!headmaskstr.empty())
+        head = select_atom(headmaskstr, (*it)->Top());
+      if (head < -1) return CpptrajState::ERR;
+      int tail = -1;
+      if (!tailmaskstr.empty())
+        tail = select_atom(tailmaskstr, (*it)->Top());
+      if (tail < -1) return CpptrajState::ERR;
+      if (head == -1 && tail == -1) {
+        mprinterr("Error: Neither head atom nor tail atom could be set via mask.\n");
+        return CpptrajState::ERR;
+      }
+      connect = AssociatedData_Connect(head, tail);
+    }
+    // Check for existing associated data
+    AssociatedData_Connect* ad = (AssociatedData_Connect*)(*it)->GetAssociatedData(AssociatedData::CONNECT);
+    if (ad == 0) {
+      (*it)->AssociateData( &connect );
+    } else {
+      mprintf("Warning: Overwriting existing connect data in '%s'.\n", (*it)->legend());
+      *ad = connect;
+    }
+  }
+
+  return CpptrajState::OK;
+}
+
 // Exec_DataSetCmd::VectorCoord()
 Exec::RetType Exec_DataSetCmd::VectorCoord(CpptrajState& State, ArgList& argIn) {
   // Keywords
@@ -883,7 +987,7 @@ Exec::RetType Exec_DataSetCmd::ChangeModeType(CpptrajState const& State, ArgList
   // Additional options for type 'noe'
   AssociatedData_NOE noeData;
   if (dtype == MetaData::NOE) {
-    if (noeData.NOE_Args(argIn))
+    if (noeData.ProcessAdataArgs(argIn))
       return CpptrajState::ERR;
   }
   if (dmode != MetaData::UNKNOWN_MODE)
@@ -912,7 +1016,15 @@ Exec::RetType Exec_DataSetCmd::ChangeModeType(CpptrajState const& State, ArgList
           mprintf("Warning: '%s': Expected 2D matrix data set type for mode '%s'\n",
                   (*ds)->legend(), MetaData::ModeString(dmode));
       }
-      if ( dtype == MetaData::NOE ) (*ds)->AssociateData( &noeData );
+      if ( dtype == MetaData::NOE ) {
+        AssociatedData_NOE* ad = (AssociatedData_NOE*)(*ds)->GetAssociatedData(AssociatedData::NOE);
+        if (ad == 0) {
+          (*ds)->AssociateData( &noeData );
+        } else {
+          mprintf("Warning: Overwriting existing NOE data for %s\n", (*ds)->legend());
+          *ad = noeData;
+        }
+      }
       mprintf("\t\t'%s'\n", (*ds)->legend());
       MetaData md = (*ds)->Meta();
       md.SetScalarMode( dmode );
diff --git a/src/Exec_DataSetCmd.h b/src/Exec_DataSetCmd.h
index d9f17149f1..5a72d97644 100644
--- a/src/Exec_DataSetCmd.h
+++ b/src/Exec_DataSetCmd.h
@@ -21,6 +21,7 @@ class Exec_DataSetCmd : public Exec {
 
     static void Help_ModifyPoints();
     RetType ModifyPoints(CpptrajState&, ArgList&, bool);
+    RetType SetConnect(CpptrajState&, ArgList&);
     RetType VectorCoord(CpptrajState&, ArgList&);
     RetType ChangeOutputFormat(CpptrajState const&, ArgList&);
     RetType Remove(CpptrajState&, ArgList&);
diff --git a/src/Exec_Graft.cpp b/src/Exec_Graft.cpp
index b948d81cb4..6a9016ff2a 100644
--- a/src/Exec_Graft.cpp
+++ b/src/Exec_Graft.cpp
@@ -1,43 +1,23 @@
 #include "Exec_Graft.h"
 #include "CpptrajStdio.h"
 #include "DataSet_Coords.h"
+#include "Structure/Builder.h"
 #include <algorithm> // std::copy
 
-// Exec_Graft::Help()
-void Exec_Graft::Help() const
-{
-  mprintf("\tsrc <source COORDS> [srcframe <#>] [srcfitmask <mask>] [srcmask <mask>]\n"
-          "\t[srccharge <charge>\n"
-          "\ttgt <target COORDS> [tgtframe <#>] [tgtfitmask <mask>] [tgtmask <mask>]\n"
-          "\t[tgtcharge <charge>\n"
-          "\tname <output COORDS> [bond <tgt>,<src> ...]\n"
-          "  Graft coordinates from source to coordinates in target.\n");
-}
+using namespace Cpptraj::Structure;
 
-/** Update indices in the given array to what the new indices will
-  * be after processing with the given mask.
-  * \return 1 if an index is not in the mask, 0 if all indices updated successfully.
-  */
-static int UpdateIndices(std::vector<int>& Idxs, AtomMask const& maskIn, int offset)
-{
-  for (std::vector<int>::iterator it = Idxs.begin();
-                                  it != Idxs.end(); ++it)
-  {
-    // Search for index in mask
-    int newidx = 0;
-    for (; newidx != maskIn.Nselected(); newidx++)
-    {
-      if (*it == maskIn[newidx]) {
-        *it = newidx + offset;
-        break;
-      }
-    }
-    if (newidx == maskIn.Nselected()) {
-      mprinterr("Error: Bonded index is in a removed section.\n");
-      return 1;
-    }
-  }
-  return 0;
+/** CONSTRUCTOR */
+Exec_Graft::Exec_Graft() :
+  Exec(COORDS),
+  debug_(0),
+  newMol0Top_(0),
+  newMol1Top_(0)
+{}
+
+/** DESTRUCTOR */
+Exec_Graft::~Exec_Graft() {
+  if (newMol0Top_ != 0) delete newMol0Top_;
+  if (newMol1Top_ != 0) delete newMol1Top_;
 }
 
 /** Redistribute charge on atoms in topology to match a target charge. */
@@ -79,42 +59,95 @@ int Exec_Graft::redistribute_charge(Topology& topIn, double charge) {
   return 0;
 }
 
-// Exec_Graft::Execute()
-Exec::RetType Exec_Graft::Execute(CpptrajState& State, ArgList& argIn)
+/** Get COORDS set. */
+DataSet_Coords* Exec_Graft::get_crd(ArgList& argIn, DataSetList const& DSL,
+                                    const char* key, const char* desc, Frame& srcFrame, const char* frameKey)
 {
-  typedef std::vector<int> Iarray;
-  // Get source coords
-  std::string kw = argIn.GetStringKey("src");
+  std::string kw = argIn.GetStringKey(key);
   if (kw.empty()) {
-    mprinterr("Error: Source COORDS must be specified with 'src'.\n");
-    return CpptrajState::ERR;
+    mprinterr("Error: %s must be specified with '%s'.\n", desc, key);
+    return 0;
   }
-  DataSet_Coords* srcCoords = (DataSet_Coords*)State.DSL().FindSetOfGroup(kw, DataSet::COORDINATES);
+  DataSet_Coords* srcCoords = (DataSet_Coords*)DSL.FindSetOfGroup(kw, DataSet::COORDINATES);
   if (srcCoords == 0) {
-    mprinterr("Error: Source COORDS %s not found.\n", kw.c_str());
-    return CpptrajState::ERR;
+    mprinterr("Error: %s %s not found.\n", desc, kw.c_str());
+    return 0;
   }
-  Frame srcFrame = srcCoords->AllocateFrame();
-  srcCoords->GetFrame(argIn.getKeyInt("srcframe", 1)-1, srcFrame);
-  bool hasSrcCharge = argIn.Contains("srccharge");
-  double srccharge = argIn.getKeyDouble("srccharge", 0);
-  // Get target coords
-  kw = argIn.GetStringKey("tgt");
-  if (kw.empty()) {
-    mprinterr("Error: Target COORDS must be specified with 'tgt'.\n");
-    return CpptrajState::ERR;
+  srcFrame = srcCoords->AllocateFrame();
+  srcCoords->GetFrame(argIn.getKeyInt(frameKey, 1)-1, srcFrame);
+  return srcCoords;
+}
+
+/** Modify given topology and frame by specified mask.
+  * \return topology modified by mask.
+  */
+Topology* Exec_Graft::modify_top(Topology const& topIn, AtomMask const& mask, Frame& srcFrame)
+                                 
+{
+  mprintf("\tAtoms to keep from '%s' : ", topIn.c_str());
+  mask.BriefMaskInfo();
+  mprintf("\n");
+
+  Topology* srcTopPtr = topIn.modifyStateByMask( mask );
+  if (srcTopPtr == 0) {
+    mprinterr("Error: Could not modify topology %s.\n", topIn.c_str());
+    return 0;
   }
-  DataSet_Coords* tgtCoords = (DataSet_Coords*)State.DSL().FindSetOfGroup(kw, DataSet::COORDINATES);
-  if (tgtCoords == 0) {
-    mprinterr("Error: Target COORDS %s not found.\n", kw.c_str());
-    return CpptrajState::ERR;
+  Frame* srcFrmPtr = new Frame();
+  srcFrmPtr->SetupFrameV(srcTopPtr->Atoms(), srcFrame.CoordsInfo());
+  srcFrmPtr->SetFrame(srcFrame, mask);
+  srcFrame = *srcFrmPtr;
+  delete srcFrmPtr;
+  return srcTopPtr;
+}
+
+/** Select bond atom index. */
+int Exec_Graft::select_bond_idx(std::string const& bond0maskstr, Topology const& mol0Top) {
+  // Select bond atom indices
+  AtomMask bondmask0;
+  if (bondmask0.SetMaskString( bond0maskstr )) return -1;
+  if (mol0Top.SetupIntegerMask( bondmask0 )) return -1;
+  if (bondmask0.None()) {
+    mprinterr("Error: Bond mask '%s' selects no atoms in topology '%s'\n", bondmask0.MaskString(), mol0Top.c_str());
+    return -1;
   }
-  Frame tgtFrame = tgtCoords->AllocateFrame();
-  tgtCoords->GetFrame(argIn.getKeyInt("tgtframe", 1)-1, tgtFrame);
-  bool hasTgtCharge = argIn.Contains("tgtcharge");
-  double tgtcharge = argIn.getKeyDouble("tgtcharge", 0);
+  if (bondmask0.Nselected() > 1) {
+    mprinterr("Error: Bond mask '%s' selects more than 1 atom in topology '%s'\n", bondmask0.MaskString(), mol0Top.c_str());
+    return -1;
+  }
+  return bondmask0[0];
+}
+
+// Exec_Graft::Help()
+void Exec_Graft::Help() const
+{
+  mprintf("\tsrc <source COORDS> [srcframe <#>] [srcmask <mask> [srccharge <charge>]]\n"
+          "\ttgt <target COORDS> [tgtframe <#>] [tgtmask <mask> [tgtcharge <charge>]]\n"
+          "\t{ic | [srcfitmask <mask>] [tgtfitmask <mask>]}\n"
+          "\tname <output COORDS> [bond <tgt>,<src> ...]\n"
+          "  Graft coordinates from source to coordinates in target.\n"
+          "  If 'ic' is specified use internal coordinates to link the coordinates,\n"
+          "  otherwise rely on rms-fitting. If 'ic' is specified, exactly 1 bond\n"
+          "  must be specified.\n");
+}
+
+// Exec_Graft::Execute()
+Exec::RetType Exec_Graft::Execute(CpptrajState& State, ArgList& argIn)
+{
+  debug_ = State.Debug();
+  bool use_ic = argIn.hasKey("ic");
+
+  // Source (1, fragment)
+  Frame mol1frm;
+  DataSet_Coords* mol1crd = get_crd(argIn, State.DSL(), "src", "Source COORDS", mol1frm, "srcframe");
+  if (mol1crd == 0) return CpptrajState::ERR;
+  // Target (0, base)
+  Frame mol0frm;
+  DataSet_Coords* mol0crd = get_crd(argIn, State.DSL(), "tgt", "Target COORDS", mol0frm, "tgtframe");
+  if (mol0crd == 0) return CpptrajState::ERR;
+
   // Create output coords
-  kw = argIn.GetStringKey("name");
+  std::string kw = argIn.GetStringKey("name");
   if (kw.empty()) {
     mprinterr("Error: Output COORDS must be specified with 'name'.\n");
     return CpptrajState::ERR;
@@ -124,92 +157,85 @@ Exec::RetType Exec_Graft::Execute(CpptrajState& State, ArgList& argIn)
     mprinterr("Error: Output COORDS %s could not be created.\n", kw.c_str());
     return CpptrajState::ERR;
   }
+ 
+  // Get atoms to bond
+  Sarray bond0ArgStrings;
+  Sarray bond1ArgStrings;
+  std::string bondargstr = argIn.GetStringKey("bond");
+  while (!bondargstr.empty()) {
+    ArgList bondarg( bondargstr, "," );
+    if (bondarg.Nargs() != 2) {
+      mprinterr("Error: Expected 2 comma-separated masks for 'bond' keyword, got %i\n", bondarg.Nargs());
+      return CpptrajState::ERR;
+    }
+    bond0ArgStrings.push_back(bondarg[0]);
+    bond1ArgStrings.push_back(bondarg[1]);
+    bondargstr = argIn.GetStringKey("bond");
+  }
+
   // Get atoms to keep from source.
-  AtomMask srcMask;
-  if (srcMask.SetMaskString( argIn.GetStringKey("srcmask") ))
+  AtomMask mol1Mask;
+  if (mol1Mask.SetMaskString( argIn.GetStringKey("srcmask") ))
     return CpptrajState::ERR;
-  if (srcCoords->Top().SetupIntegerMask(srcMask))
+  if (mol1crd->Top().SetupIntegerMask(mol1Mask))
     return CpptrajState::ERR;
   // Get atoms to keep from target.
-  AtomMask tgtMask;
-  if (tgtMask.SetMaskString( argIn.GetStringKey("tgtmask") ))
-    return CpptrajState::ERR;
-  if (tgtCoords->Top().SetupIntegerMask(tgtMask))
-    return CpptrajState::ERR;
-  // Get bonds
-  Iarray tgtBondAtoms, srcBondAtoms;
-  kw = argIn.GetStringKey("bond");
-  while (!kw.empty()) {
-    ArgList bndarg(kw, ",");
-    if (bndarg.Nargs() != 2) {
-      mprinterr("Error: Expected 2 atom masks for 'bond' (target, source).\n");
-      return CpptrajState::ERR;
-    }
-    AtomMask tb, sb;
-    if (tb.SetMaskString(bndarg[0])) return CpptrajState::ERR;
-    if (sb.SetMaskString(bndarg[1])) return CpptrajState::ERR;
-    if (tgtCoords->Top().SetupIntegerMask(tb)) return CpptrajState::ERR;
-    if (srcCoords->Top().SetupIntegerMask(sb)) return CpptrajState::ERR;
-    if (tb.Nselected() != 1) {
-      mprinterr("Error: 'bond' target mask does not select only 1 atom.\n");
-      return CpptrajState::ERR;
-    }
-    if (sb.Nselected() != 1) {
-      mprinterr("Error: 'bond' source mask does not select only 1 atom.\n");
-      return CpptrajState::ERR;
-    }
-    tgtBondAtoms.push_back( tb[0] );
-    srcBondAtoms.push_back( sb[0] );
-    mprintf("\tWill bond target %s (%i) to source %s (%i)\n",
-            tb.MaskString(), tgtBondAtoms.back()+1,
-            sb.MaskString(), srcBondAtoms.back()+1);
-    kw = argIn.GetStringKey("bond");
-  }
-  // Update the bond indices for the new topologies
-  if (UpdateIndices(tgtBondAtoms, tgtMask, 0))
+  AtomMask mol0Mask;
+  if (mol0Mask.SetMaskString( argIn.GetStringKey("tgtmask") ))
     return CpptrajState::ERR;
-  if (UpdateIndices(srcBondAtoms, srcMask, tgtMask.Nselected()))
+  if (mol0crd->Top().SetupIntegerMask(mol0Mask))
     return CpptrajState::ERR;
-  mprintf("\tUpdated bond indices:\n");
-  for (unsigned int ii = 0; ii != tgtBondAtoms.size(); ii++)
-    mprintf("\t  tgt= %i  src= %i\n", tgtBondAtoms[ii]+1, srcBondAtoms[ii]+1);
+
+  // Determine if charges will be redistributed
+  bool hasSrcCharge = argIn.Contains("srccharge");
+  double srccharge = argIn.getKeyDouble("srccharge", 0);
+  bool hasTgtCharge = argIn.Contains("tgtcharge");
+  double tgtcharge = argIn.getKeyDouble("tgtcharge", 0);
+
   // Get atoms from source to fit on target, and atoms from target
   // for source to fit on.
   AtomMask srcFitMask, tgtFitMask;
-  std::string srcfitstr = argIn.GetStringKey("srcfitmask");
-  std::string tgtfitstr = argIn.GetStringKey("tgtfitmask");
   bool doRmsFit = false;
-  if (!srcfitstr.empty() || !tgtfitstr.empty()) {
-    doRmsFit = true;
-    // If either is empty, fill with the other.
-    if (srcfitstr.empty())
-      srcfitstr = tgtfitstr;
-    else if (tgtfitstr.empty())
-      tgtfitstr = srcfitstr;
-    if (srcFitMask.SetMaskString( srcfitstr ))
-      return CpptrajState::ERR;
-    if (tgtFitMask.SetMaskString( tgtfitstr ))
-      return CpptrajState::ERR;
-    // Set up the masks.
-    if (srcCoords->Top().SetupIntegerMask(srcFitMask))
-      return CpptrajState::ERR;
-    if (tgtCoords->Top().SetupIntegerMask(tgtFitMask))
-      return CpptrajState::ERR;
+  if (!use_ic) { // TODO allow with IC?
+    std::string srcfitstr = argIn.GetStringKey("srcfitmask");
+    std::string tgtfitstr = argIn.GetStringKey("tgtfitmask");
+    if (!srcfitstr.empty() || !tgtfitstr.empty()) {
+      doRmsFit = true;
+      // If either is empty, fill with the other.
+      if (srcfitstr.empty())
+        srcfitstr = tgtfitstr;
+      else if (tgtfitstr.empty())
+        tgtfitstr = srcfitstr;
+      if (srcFitMask.SetMaskString( srcfitstr ))
+        return CpptrajState::ERR;
+      if (tgtFitMask.SetMaskString( tgtfitstr ))
+        return CpptrajState::ERR;
+      // Set up the masks.
+      if (mol1crd->Top().SetupIntegerMask(srcFitMask))
+        return CpptrajState::ERR;
+      if (mol0crd->Top().SetupIntegerMask(tgtFitMask))
+        return CpptrajState::ERR;
+    }
   }
-  
+
   // Info
-  mprintf("\tSource coords   : %s\n", srcCoords->legend());
-  mprintf("\tTarget coords   : %s\n", tgtCoords->legend());
+  mprintf("\tSource coords   : %s\n", mol1crd->legend());
+  mprintf("\tTarget coords   : %s\n", mol0crd->legend());
   mprintf("\tOutput coords   : %s\n", outCoords->legend());
   mprintf("\tSource mask     :");
-  srcMask.BriefMaskInfo();
+  mol1Mask.BriefMaskInfo();
   mprintf("\n");
   mprintf("\tTarget mask     :");
-  tgtMask.BriefMaskInfo();
+  mol0Mask.BriefMaskInfo();
   mprintf("\n");
-  if (hasSrcCharge && (srcMask.Nselected() != srcCoords->Top().Natom()))
+  if (!bond0ArgStrings.empty()) {
+    mprintf("\tBonds will be created between:\n");
+    for (unsigned int idx = 0; idx != bond0ArgStrings.size(); idx++)
+      mprintf("\t\tAtoms %s and %s\n", bond0ArgStrings[idx].c_str(), bond1ArgStrings[idx].c_str());
+  }
+  if (hasSrcCharge && (mol1Mask.Nselected() != mol1crd->Top().Natom()))
     mprintf("\tAdjusting source charge to %g\n", srccharge);
-  if (hasTgtCharge && (tgtMask.Nselected() != tgtCoords->Top().Natom()))
+  if (hasTgtCharge && (mol0Mask.Nselected() != mol0crd->Top().Natom()))
     mprintf("\tAdjusting target charge to %g\n", tgtcharge);
   if (doRmsFit) {
     mprintf(  "\tSource fit mask :");
@@ -223,93 +249,163 @@ Exec::RetType Exec_Graft::Execute(CpptrajState& State, ArgList& argIn)
     }
     // Source gets RMS fit to target (reference)
     Frame srcFitFrame;
-    srcFitFrame.SetupFrameFromMask(srcFitMask, srcCoords->Top().Atoms());
-    srcFitFrame.SetCoordinates(srcFrame, srcFitMask);
+    srcFitFrame.SetupFrameFromMask(srcFitMask, mol1crd->Top().Atoms());
+    srcFitFrame.SetCoordinates(mol1frm, srcFitMask);
     Frame tgtFitFrame;
-    tgtFitFrame.SetupFrameFromMask(tgtFitMask, tgtCoords->Top().Atoms());
-    tgtFitFrame.SetCoordinates(tgtFrame, tgtFitMask);
+    tgtFitFrame.SetupFrameFromMask(tgtFitMask, mol0crd->Top().Atoms());
+    tgtFitFrame.SetCoordinates(mol0frm, tgtFitMask);
     Vec3 refTrans = tgtFitFrame.CenterOnOrigin(false);
     Matrix_3x3 Rot;
     Vec3 Trans;
     srcFitFrame.RMSD_CenteredRef( tgtFitFrame, Rot, Trans, false );
-    srcFrame.Trans_Rot_Trans( Trans, Rot, refTrans );
+    mol1frm.Trans_Rot_Trans( Trans, Rot, refTrans );
   }
 
-  // Modify source if needed.
-  Topology* srcTopPtr = srcCoords->TopPtr();
-  Frame*    srcFrmPtr = &srcFrame;
-  if (srcMask.Nselected() != srcCoords->Top().Natom()) {
-    srcTopPtr = srcCoords->Top().modifyStateByMask( srcMask );
-    if (srcTopPtr == 0) {
-      mprinterr("Error: Could not modify source topology.\n");
-      return CpptrajState::ERR;
+  // Modify the target (mol0) topology
+  if (newMol0Top_ != 0) delete newMol0Top_;
+  newMol0Top_ = 0;
+  Topology* mol0Top = 0;
+  if (mol0Mask.Nselected() == mol0crd->Top().Natom()) {
+    mol0Top = mol0crd->TopPtr();
+  } else {
+    mol0Top = modify_top(mol0crd->Top(), mol0Mask, mol0frm);
+    newMol0Top_ = mol0Top;
+    if (mol0Top == 0) return CpptrajState::ERR;
+    // Modify charges if needed
+    if (hasTgtCharge) {
+      if (redistribute_charge(*mol0Top, tgtcharge)) {
+        mprinterr("Error: Redistribute tgt charge failed.\n");
+        return CpptrajState::ERR;
+      }
     }
-    srcFrmPtr = new Frame();
-    srcFrmPtr->SetupFrameV(srcTopPtr->Atoms(), srcCoords->CoordsInfo());
-    srcFrmPtr->SetFrame(srcFrame, srcMask);
+  }
+  // Modify the source (mol1) topology
+  if (newMol1Top_ != 0) delete newMol1Top_;
+  newMol1Top_ = 0;
+  Topology* mol1Top = 0;
+  if (mol1Mask.Nselected() == mol1crd->Top().Natom()) {
+    mol1Top = mol1crd->TopPtr();
+  } else {
+    mol1Top = modify_top(mol1crd->Top(), mol1Mask, mol1frm);
+    newMol1Top_ = mol1Top;
+    if (mol1Top == 0) return CpptrajState::ERR;
     // Modify charges if needed
     if (hasSrcCharge) {
-      if (redistribute_charge(*srcTopPtr, srccharge)) {
+      if (redistribute_charge(*mol1Top, srccharge)) {
         mprinterr("Error: Redistribute src charge failed.\n");
         return CpptrajState::ERR;
       }
     }
   }
 
-  // Modify target if needed.
-  Topology* tgtTopPtr = tgtCoords->TopPtr();
-  Frame*    tgtFrmPtr = &tgtFrame;
-  if (tgtMask.Nselected() != tgtCoords->Top().Natom()) {
-    tgtTopPtr = tgtCoords->Top().modifyStateByMask( tgtMask );
-    if (tgtTopPtr == 0) {
-      mprinterr("Error: Could not modify target topology.\n");
+  if (use_ic) {
+    if (graft_ic( outCoords, *mol0Top, mol0frm, *mol1Top, mol1frm, bond0ArgStrings, bond1ArgStrings))
+      return CpptrajState::ERR;
+  } else {
+    if (graft_rms( outCoords, *mol0Top, mol0frm, *mol1Top, mol1frm, bond0ArgStrings, bond1ArgStrings))
       return CpptrajState::ERR;
-    }
-    tgtFrmPtr = new Frame();
-    tgtFrmPtr->SetupFrameV(tgtTopPtr->Atoms(), tgtCoords->CoordsInfo());
-    tgtFrmPtr->SetFrame(tgtFrame, tgtMask);
-    // Modify charges if needed
-    if (hasTgtCharge) {
-      if (redistribute_charge(*tgtTopPtr, tgtcharge)) {
-        mprinterr("Error: Redistribute tgt charge failed.\n");
-        return CpptrajState::ERR;
-      }
-    }
   }
+  return CpptrajState::OK;
+}
 
+
+/** Graft using internal coordinates to build the final structure. */
+int Exec_Graft::graft_ic(DataSet_Coords* outCoords,
+                         Topology const& mol0Top, Frame const& mol0frm,
+                         Topology const& mol1Top, Frame const& mol1frm,
+                         Sarray const& bond0Atoms, Sarray const& bond1Atoms)
+const
+{
+  // Get bonding atom masks
+  if (bond0Atoms.size() != 1 || bond1Atoms.size() != 1) {
+    mprinterr("Error: Graft with internal coordinates only works with 1 bond.\n");
+    return 1;
+  }
+  std::string const& tgtbondmask = bond0Atoms[0];
+  std::string const& srcbondmask = bond1Atoms[0];
+
+  // Select bond atom indices
+  int bondat0 = select_bond_idx(tgtbondmask, mol0Top);
+  if (bondat0 < 0) {
+    mprinterr("Error: Could not select target bond atom '%s'\n", tgtbondmask.c_str());
+    return 1;
+  }
+  int bondat1 = select_bond_idx(srcbondmask, mol1Top);
+  if (bondat1 < 0) {
+    mprinterr("Error: Could not select source bond atom '%s'\n", srcbondmask.c_str());
+    return 1;
+  }
+
+  // Combine topologies.
+  Topology combinedTop;
+  combinedTop.SetDebug( debug_ );
+  combinedTop.SetParmName( outCoords->Meta().Name(), FileName() );
+  combinedTop.AppendTop( mol0Top );
+  combinedTop.SetParmBox( mol0frm.BoxCrd() );
+  if (debug_ > 0)
+    combinedTop.Brief("Grafted parm:");
+
+  Frame CombinedFrame = mol0frm;
+  Builder builder;
+  builder.SetDebug( debug_ );
+  if (builder.Combine( combinedTop, CombinedFrame, mol1Top, mol1frm, bondat0, bondat1 )) {
+    mprinterr("Error: Fragment combine failed.\n");
+    return 1;
+  }
+
+  // Add topology to output COORDS set
+  if (outCoords->CoordsSetup(combinedTop, CombinedFrame.CoordsInfo())) return 1;
+
+  // Add frame to the output data set
+  outCoords->AddFrame( CombinedFrame );
+
+  return 0;
+}
+
+/** Graft with RMS-fitting. */
+int Exec_Graft::graft_rms(DataSet_Coords* outCoords,
+                                    Topology const& mol0Top, Frame const& mol0frm,
+                                    Topology const& mol1Top, Frame const& mol1frm,
+                                    Sarray const& bond0Atoms, Sarray const& bond1Atoms)
+const
+{
   // Combine topologies. Use target box info.
   Topology combinedTop;
-  combinedTop.SetDebug( State.Debug() );
+  combinedTop.SetDebug( debug_ );
   combinedTop.SetParmName( outCoords->Meta().Name(), FileName() );
-  combinedTop.AppendTop( *tgtTopPtr );
-  combinedTop.AppendTop( *srcTopPtr );
+  combinedTop.AppendTop( mol0Top );
+  combinedTop.AppendTop( mol1Top );
+
   // Add any bonds
-  for (unsigned int ii = 0; ii != tgtBondAtoms.size(); ii++)
-    combinedTop.AddBond( tgtBondAtoms[ii], srcBondAtoms[ii] );
+  for (unsigned int ii = 0; ii != bond0Atoms.size(); ii++) {
+    int bondat0 = select_bond_idx(bond0Atoms[ii], mol0Top);
+    if (bondat0 < 0) {
+      mprinterr("Error: Could not select target bond atom '%s'\n", bond0Atoms[ii].c_str());
+      return 1;
+    }
+    int bondat1 = select_bond_idx(bond1Atoms[ii], mol1Top);
+    if (bondat1 < 0) {
+      mprinterr("Error: Could not select source bond atom '%s'\n", bond1Atoms[ii].c_str());
+      return 1;
+    }
+    combinedTop.AddBond( bondat0, bondat1 + mol0Top.Natom() ); // TODO pseudo-parameter?
+  }
   // Regenerate the molecule info FIXME should Topology just do this?
-  if (combinedTop.DetermineMolecules()) return CpptrajState::ERR;
-  combinedTop.SetParmBox( tgtFrmPtr->BoxCrd() );
+  if (combinedTop.DetermineMolecules()) return 1;
+  combinedTop.SetParmBox( mol0frm.BoxCrd() );
   combinedTop.Brief("Grafted parm:");
-
-  // Output coords.
   // Only coords+box for now.
-  CoordinateInfo outInfo(tgtFrmPtr->BoxCrd(), false, false, false);
-  if (outCoords->CoordsSetup(combinedTop, outInfo)) return CpptrajState::ERR;
+  CoordinateInfo outInfo(mol0frm.BoxCrd(), false, false, false);
+  if (outCoords->CoordsSetup(combinedTop, outInfo)) return 1;
+
+  // Combine coords.
   Frame CombinedFrame = outCoords->AllocateFrame();
-  std::copy(tgtFrmPtr->xAddress(), tgtFrmPtr->xAddress()+tgtFrmPtr->size(), CombinedFrame.xAddress());
-  std::copy(srcFrmPtr->xAddress(), srcFrmPtr->xAddress()+srcFrmPtr->size(), CombinedFrame.xAddress()+tgtFrmPtr->size());
-  CombinedFrame.SetBox( tgtFrmPtr->BoxCrd() );
-  outCoords->AddFrame( CombinedFrame );
+  std::copy(mol0frm.xAddress(), mol0frm.xAddress()+mol0frm.size(), CombinedFrame.xAddress());
+  std::copy(mol1frm.xAddress(), mol1frm.xAddress()+mol1frm.size(), CombinedFrame.xAddress()+mol0frm.size());
+  CombinedFrame.SetBox( mol0frm.BoxCrd() );
 
-  // Free memory if needed
-  if (srcTopPtr != srcCoords->TopPtr()) {
-    delete srcTopPtr;
-    delete srcFrmPtr;
-  }
-  if (tgtTopPtr != tgtCoords->TopPtr()) {
-    delete tgtTopPtr;
-    delete tgtFrmPtr;
-  }
+  // Add to topology
+  outCoords->AddFrame( CombinedFrame );
 
-  return CpptrajState::OK;
+  return 0;
 }
diff --git a/src/Exec_Graft.h b/src/Exec_Graft.h
index 91a5d4871d..1df79f08b3 100644
--- a/src/Exec_Graft.h
+++ b/src/Exec_Graft.h
@@ -4,11 +4,29 @@
 /// Graft part of one COORDS to another COORDS 
 class Exec_Graft : public Exec {
   public:
-    Exec_Graft() : Exec(COORDS) {}
+    Exec_Graft();
+    ~Exec_Graft();
     void Help() const;
     DispatchObject* Alloc() const { return (DispatchObject*)new Exec_Graft(); }
     RetType Execute(CpptrajState&, ArgList&);
   private:
+    typedef std::vector<int> Iarray;
+    typedef std::vector<std::string> Sarray;
+    /// Select bond index from expression in given topology
+    static int select_bond_idx(std::string const&, Topology const&); 
+    /// Redistribute charge in given topology to match given target
     static int redistribute_charge(Topology&, double);
+    /// Modify topology and frame according to mask expression
+    static Topology* modify_top(Topology const&, AtomMask const&, Frame&);
+    /// Get COORDS data set
+    static DataSet_Coords* get_crd(ArgList&, DataSetList const&, const char*, const char*, Frame&, const char*);
+    /// Graft using internal coordinates
+    int graft_ic(DataSet_Coords*, Topology const&, Frame const&, Topology const&, Frame const&, Sarray const&, Sarray const&) const;
+    /// Graft assuming structures have been rms fit
+    int graft_rms(DataSet_Coords*, Topology const&, Frame const&, Topology const&, Frame const&, Sarray const&, Sarray const&) const;
+
+    int debug_;
+    Topology* newMol0Top_; ///< Hold target topology if modified.
+    Topology* newMol1Top_; ///< Hold source topology if modified.
 };
 #endif
diff --git a/src/Exec_Sequence.cpp b/src/Exec_Sequence.cpp
new file mode 100644
index 0000000000..63a69b2bf1
--- /dev/null
+++ b/src/Exec_Sequence.cpp
@@ -0,0 +1,187 @@
+#include "Exec_Sequence.h"
+#include "CpptrajStdio.h"
+#include "AssociatedData_Connect.h"
+#include "Structure/Builder.h"
+
+/** Generate and build the specified sequence. */
+int Exec_Sequence::generate_sequence(DataSet_Coords* OUT,
+                                     DataSetList const& DSL,
+                                     Sarray const& main_sequence,
+                                     Sarray const& LibSetNames)
+const
+{
+  // First, get all units in order.
+  typedef std::vector<DataSet_Coords*> Uarray;
+  Uarray Units;
+  Units.reserve( main_sequence.size() );
+  typedef std::vector<int> Iarray;
+  Iarray connectAt0, connectAt1;
+  connectAt0.reserve( Units.size() );
+  connectAt1.reserve( Units.size() );
+  int total_natom = 0;
+
+  for (Sarray::const_iterator it = main_sequence.begin(); it != main_sequence.end(); ++it)
+  {
+    DataSet_Coords* unit = 0;
+    if (LibSetNames.empty()) {
+      // Look for name
+      unit = (DataSet_Coords*)DSL.FindSetOfGroup( *it, DataSet::COORDINATES );
+    } else {
+      // Look for name[aspect]
+      DataSet* ds = 0;
+      for (Sarray::const_iterator name = LibSetNames.begin(); name != LibSetNames.end(); ++name)
+      {
+        MetaData meta(*name, *it);
+        ds = DSL.CheckForSet( meta );
+        if (ds != 0) break;
+      }
+      if (ds != 0) {
+        if (ds->Group() != DataSet::COORDINATES) {
+          mprinterr("Error: Set '%s' is not of type Coordinates.\n", ds->legend());
+          return 1;
+        }
+        unit = (DataSet_Coords*)ds;
+      }
+    }
+    if (unit == 0) {
+      mprinterr("Error: Unit '%s' not found.\n", it->c_str());
+      return 1;
+    }
+    if (unit->Size() < 1) {
+      mprinterr("Error: Unit '%s' is empty.\n", unit->legend());
+      return 1;
+    }
+    if (unit->Size() > 1) {
+      mprintf("Warning: Unit '%s' has more than 1 frame. Only using first frame.\n", unit->legend());
+    }
+    // Needs to have connect associated data
+    AssociatedData* ad = unit->GetAssociatedData(AssociatedData::CONNECT);
+    if (ad == 0) {
+      mprinterr("Error: Unit '%s' does not have CONNECT data.\n", unit->legend());
+      return 1;
+    }
+    AssociatedData_Connect const& C = static_cast<AssociatedData_Connect const&>( *ad );
+    if (C.NconnectAtoms() < 2) {
+      mprinterr("Error: Not enough connect atoms in unit '%s'\n", unit->legend());
+      return 1;
+    }
+    // Update connect atom 1 indices based on their position in the sequence.
+    // Do not update connect atom 0 indices since they will not yet be connected.
+    connectAt0.push_back( C.Connect()[0] );
+    connectAt1.push_back( C.Connect()[1] + total_natom );
+    Units.push_back( unit );
+    total_natom += unit->Top().Natom();
+  } // END loop over sequence
+  mprintf("\tFound %zu units.\n", Units.size());
+  if (Units.empty()) {
+    mprinterr("Error: No units.\n");
+    return 1;
+  }
+  for (unsigned int idx = 0; idx < Units.size(); idx++)
+    mprintf("\tUnit %s HEAD %i TAIL %i\n", Units[idx]->legend(), connectAt0[idx]+1, connectAt1[idx]+1);
+
+  Topology combinedTop;
+  combinedTop.SetDebug( debug_ );
+  combinedTop.SetParmName( OUT->Meta().Name(), FileName() );
+  combinedTop.AppendTop( Units.front()->Top() );
+  //combinedTop.SetParmBox( Units // TODO
+  combinedTop.Brief("Sequence topology:");
+
+  Frame CombinedFrame = Units.front()->AllocateFrame();
+  Units.front()->GetFrame(0, CombinedFrame);
+
+
+  using namespace Cpptraj::Structure;
+  Builder builder;
+  for (unsigned int idx = 1; idx < Units.size(); idx++) {
+    mprintf("\tConnect %s atom %i to %s atom %i\n",
+            Units[idx-1]->legend(), connectAt1[idx-1]+1,
+            Units[idx]->legend(),   connectAt0[idx]  +1);
+    Frame mol1frm = Units[idx]->AllocateFrame();
+    Units[idx]->GetFrame(0, mol1frm);
+    int bondat0 = connectAt1[idx-1];
+    int bondat1 = connectAt0[idx];
+    if (bondat0 < 0 || bondat1 < 0) {
+      mprinterr("Error: Invalid connect atom(s) between %s atom %i to %s atom %i\n",
+                Units[idx-1]->legend(), bondat0+1, Units[idx]->legend(), bondat1+1);
+      return 1;
+    }
+    if (builder.Combine( combinedTop, CombinedFrame, Units[idx]->Top(), mol1frm,
+                         connectAt1[idx-1], connectAt0[idx] )) {
+      mprinterr("Error: Sequence combine between units %u %s and %u %s failed.\n",
+                idx, Units[idx-1]->legend(), idx+1, Units[idx]->legend());
+      return 1;
+    }
+  }
+
+  OUT->CoordsSetup(combinedTop, CombinedFrame.CoordsInfo());
+  OUT->AddFrame( CombinedFrame );
+
+  return 0;
+}
+
+// Exec_Sequence::Help()
+void Exec_Sequence::Help() const
+{
+  mprintf("\tname <output set name> <unit0> <unit1> ...\n"
+          "\t[{libset <libsetname>} ...]\n"
+          "  Create a molecule from a sequence of units.\n");
+}
+
+
+// Exec_Sequence::Execute()
+Exec::RetType Exec_Sequence::Execute(CpptrajState& State, ArgList& argIn)
+{
+  debug_ = State.Debug();
+  // Args
+  Sarray LibSetNames;
+  std::string libsetname = argIn.GetStringKey("libset");
+  while (!libsetname.empty()) {
+    LibSetNames.push_back( libsetname );
+    libsetname = argIn.GetStringKey("libset");
+  }
+  std::string dsname = argIn.GetStringKey("name");
+  if (dsname.empty()) {
+    mprinterr("Error: No output set name specified with 'name'\n");
+    return CpptrajState::ERR;
+  }
+  DataSet_Coords* OUT = (DataSet_Coords*)State.DSL().AddSet(DataSet::COORDS, MetaData(dsname));
+  if (OUT == 0) {
+    mprinterr("Error: Could not create output COORDS set named '%s'\n", dsname.c_str());
+    return CpptrajState::ERR;
+  }
+
+  // Get the actual sequence from remaining args.
+  Sarray main_sequence;
+  ArgList remaining = argIn.RemainingArgs();
+  std::string unit = remaining.GetStringNext();
+  while (!unit.empty()) {
+    main_sequence.push_back( unit );
+    unit = remaining.GetStringNext();
+  }
+  if (main_sequence.empty()) {
+    mprinterr("Error: No units specified.\n");
+    return CpptrajState::ERR;
+  }
+
+  // Info
+  if (!LibSetNames.empty()) {
+    mprintf("\tLibrary set names:");
+    for (Sarray::const_iterator it = LibSetNames.begin(); it != LibSetNames.end(); ++it)
+      mprintf(" %s", it->c_str());
+    mprintf("\n");
+  }
+  mprintf("\tMain sequence:");
+  for (Sarray::const_iterator it = main_sequence.begin(); it != main_sequence.end(); ++it)
+    mprintf(" %s", it->c_str());
+  mprintf("\n");
+  mprintf("\tOutput set name : %s\n", OUT->legend());
+
+  // Execute
+  if (generate_sequence(OUT, State.DSL(), main_sequence, LibSetNames)) {
+    mprinterr("Error: Could not generate sequence.\n");
+    return CpptrajState::ERR;
+  }
+
+  return CpptrajState::OK;
+}
diff --git a/src/Exec_Sequence.h b/src/Exec_Sequence.h
new file mode 100644
index 0000000000..148cf4e1af
--- /dev/null
+++ b/src/Exec_Sequence.h
@@ -0,0 +1,19 @@
+#ifndef INC_EXEC_SEQUENCE_H
+#define INC_EXEC_SEQUENCE_H
+#include "Exec.h"
+/// Create a molecule from a sequence of units 
+class Exec_Sequence : public Exec {
+  public:
+    Exec_Sequence() : Exec(COORDS), debug_(0) {}
+    void Help() const;
+    DispatchObject* Alloc() const { return (DispatchObject*)new Exec_Sequence(); }
+    RetType Execute(CpptrajState&, ArgList&);
+  private:
+    typedef std::vector<std::string> Sarray;
+
+    int generate_sequence(DataSet_Coords*, DataSetList const&,
+                          Sarray const&, Sarray const&) const;
+
+    int debug_;
+};
+#endif
diff --git a/src/Exec_Zmatrix.cpp b/src/Exec_Zmatrix.cpp
new file mode 100644
index 0000000000..16b643c408
--- /dev/null
+++ b/src/Exec_Zmatrix.cpp
@@ -0,0 +1,159 @@
+#include "Exec_Zmatrix.h"
+#include "CpptrajStdio.h"
+#include "DataSet_Zmatrix.h"
+#include "Structure/Zmatrix.h"
+
+using namespace Cpptraj::Structure;
+
+/** Get Zmatrix for specified molecule at specified frame number. */
+int Exec_Zmatrix::getZmatrix(DataSet_Coords* CRD, int molnum, int frmidx,
+                             std::string const& dsname, DataFile* outfile, CpptrajState& State)
+const
+{
+ if (CRD == 0) {
+    mprinterr("Error: No COORDS set specified.\n");
+    return CpptrajState::ERR;
+  }
+  mprintf("\tGetting Z-matrix from set '%s'\n", CRD->legend());
+  if (CRD->Size() < 1) {
+    mprinterr("Error: Set '%s' is empty.\n", CRD->legend());
+    return 1; 
+  }
+
+  DataSet_Zmatrix* zset = (DataSet_Zmatrix*)State.DSL().AddSet( DataSet::ZMATRIX, dsname, "ZMATRIX" );
+  if (zset == 0) {
+    mprinterr("Error: Could not allocate zmatrix set.\n");
+    return 1; 
+  }
+  zset->SetDim(Dimension::X, Dimension(1, 1, "IC"));
+  if (outfile != 0)
+    outfile->AddDataSet( zset );
+
+  mprintf("\tOutput set  : %s\n", zset->legend());
+  mprintf("\tMolecule    : %i\n", molnum + 1 );
+  mprintf("\tFrame       : %i\n", frmidx + 1 );
+  if (outfile != 0)
+    mprintf("\tOutput file : %s\n", outfile->DataFilename().full());
+
+  Frame frmIn = CRD->AllocateFrame();
+  CRD->GetFrame( frmidx, frmIn );
+
+  Zmatrix& zmatrix = *(zset->Zptr());
+
+  zmatrix.SetDebug( State.Debug() );
+  int errStat = zmatrix.SetFromFrame( frmIn, CRD->Top(), molnum );
+  if (debug_ > 0) zmatrix.print(); // DEBUG
+  return errStat;
+}
+
+/** Create COORDS using Zmatrix. */
+int Exec_Zmatrix::putZmatrix(DataSet_Coords* CRD, Topology* topIn,
+                             std::string const& zsetname,
+                             std::string const& dsname, CpptrajState& State)
+const
+{
+  // Get zmatrix set
+  DataSet_Zmatrix* zmatrix = (DataSet_Zmatrix*)State.DSL().FindSetOfType( zsetname, DataSet::ZMATRIX );
+  if (zmatrix == 0) {
+    mprinterr("Error: No zmatrix set with name '%s' found.\n", zsetname.c_str());
+    return 1;
+  }
+  mprintf("\tCreating COORDS from Zmatrix set : %s\n", zmatrix->legend());
+
+  // Create COORDS set
+  DataSet_Coords* out = (DataSet_Coords*)State.DSL().AddSet(DataSet::COORDS, dsname, "ZMCRD");
+  if (out == 0) {
+    mprinterr("Error: Could not create COORDS set for assigning from Zmatrix.\n");
+    return 1;
+  }
+  mprintf("\tOutput COORDS set: %s\n", out->legend());
+
+  Topology* myTop = 0;
+  if (topIn != 0) {
+    mprintf("\tTopology: %s\n", topIn->c_str());
+    myTop = topIn;
+  } else if (CRD != 0) {
+    mprintf("\tTopology from COORDS set: %s\n", CRD->legend());
+    myTop = CRD->TopPtr();
+  } else {
+    mprinterr("Error: No COORDS set or Topology specified for 'zset'.\n");
+    return 1;
+  }
+  CoordinateInfo myInfo;
+  if (CRD != 0)
+    myInfo = CRD->CoordsInfo();
+  out->CoordsSetup( *myTop, myInfo);
+
+  // Assign
+  Frame frm = out->AllocateFrame();
+  frm.ZeroCoords();
+  int err = 0;
+  if (debug_ > 0) {
+    Zmatrix tmpZ = *(zmatrix->Zptr()); // TODO just pass debug level into Zmatrix?
+    tmpZ.SetDebug( debug_ );
+    err = tmpZ.SetToFrame( frm );
+  } else {
+    err = zmatrix->Zptr()->SetToFrame( frm );
+  }
+  if (err != 0) {
+    mprinterr("Error: Zmatrix to Cartesian coords failed.\n");
+    return 1;
+  }
+  out->SetCRD(0, frm);
+
+  return 0;
+}
+
+// Exec_Zmatrix::Help()
+void Exec_Zmatrix::Help() const
+{
+  mprintf("\t<COORDS set name> [name <output set name>]\n"
+          "\t{ zset <input zmatrix set> [parm <top>|parmindex <#>] |\n"
+          "\t  [molnum <mol#>] [frame <frame#>] [out <zmatrix file>] }\n"
+          "  If 'zset' is specified, use Z-matrix to generate coordinates using\n"
+          "  a specified topology or topology from specified COORDS set;\n"
+          "  output is a new COORDS set.\n"
+          "  Otherwise calculate Zmatrix for specified molecule/frame of\n"
+          "  specified COORDS set; output is a Z-matrix set.\n");
+}
+
+// Exec_Zmatrix::Execute()
+Exec::RetType Exec_Zmatrix::Execute(CpptrajState& State, ArgList& argIn)
+{
+  debug_ = State.Debug();
+  std::string dsname = argIn.GetStringKey("name");
+  std::string zsetname = argIn.GetStringKey("zset");
+  int molnum = -1;
+  int frmidx = -1;
+  DataFile* outfile = 0;
+  Topology* topIn = 0;
+  if (zsetname.empty()) {
+    // Calculating Z-matrix
+    molnum = argIn.getKeyInt("molnum", 1) - 1;
+    frmidx = argIn.getKeyInt("frame", 1) - 1;
+    outfile = State.DFL().AddDataFile( argIn.GetStringKey("out"), argIn );
+  } else {
+    // Applying Zmatrix
+    if (argIn.Contains("parm") || argIn.Contains("parmindex"))
+      topIn = (Topology*)State.DSL().GetTopology(argIn);
+  }
+  // Get COORDS set name
+  std::string setname = argIn.GetStringNext();
+  // ----- No more args below here -----
+  if (setname.empty()) {
+    mprinterr("Error: %s: Specify COORDS dataset name.\n", argIn.Command());
+    return CpptrajState::ERR;
+  }
+  DataSet_Coords* CRD = (DataSet_Coords*)State.DSL().FindSetOfGroup( setname, DataSet::COORDINATES );
+
+
+  int errStat = 0;
+  if (!zsetname.empty()) {
+    errStat = putZmatrix(CRD, topIn, zsetname, dsname, State);
+  } else {
+    errStat = getZmatrix(CRD, molnum, frmidx, dsname, outfile, State);
+  }
+
+  if (errStat != 0) return CpptrajState::ERR;
+  return CpptrajState::OK;
+}
diff --git a/src/Exec_Zmatrix.h b/src/Exec_Zmatrix.h
new file mode 100644
index 0000000000..0b89547724
--- /dev/null
+++ b/src/Exec_Zmatrix.h
@@ -0,0 +1,17 @@
+#ifndef INC_EXEC_ZMATRIX_H
+#define INC_EXEC_ZMATRIX_H
+#include "Exec.h"
+/// Calculate a Zmatrix from a COORDS data set 
+class Exec_Zmatrix : public Exec {
+  public:
+    Exec_Zmatrix() : Exec(COORDS), debug_(0) {}
+    void Help() const;
+    DispatchObject* Alloc() const { return (DispatchObject*)new Exec_Zmatrix(); }
+    RetType Execute(CpptrajState&, ArgList&);
+  private:
+    int getZmatrix(DataSet_Coords*, int, int, std::string const&, DataFile*, CpptrajState&) const;
+    int putZmatrix(DataSet_Coords*, Topology*, std::string const&, std::string const&, CpptrajState&) const;
+
+    int debug_;
+};
+#endif
diff --git a/src/Frame.cpp b/src/Frame.cpp
index ef3f206fcc..8a63853801 100644
--- a/src/Frame.cpp
+++ b/src/Frame.cpp
@@ -368,7 +368,7 @@ void Frame::CopyFrom(Frame const& tgtIn, Unit const& unit) {
 }
 
 // ---------- FRAME MEMORY ALLOCATION/REALLOCATION -----------------------------
-/** \return True if reallocation of coordinate arrray must occur based on 
+/** \return True if reallocation of coordinate array must occur based on 
   *         given number of atoms.
   */
 bool Frame::ReallocateX(int natomIn) {
diff --git a/src/PotentialFunction.cpp b/src/PotentialFunction.cpp
index acb1ff5e9b..5d2e66a2d4 100644
--- a/src/PotentialFunction.cpp
+++ b/src/PotentialFunction.cpp
@@ -9,6 +9,12 @@
 #include "PotentialTerm_Angle.h"
 #include "PotentialTerm_Dihedral.h"
 
+/** DESTRUCTOR */
+PotentialFunction::~PotentialFunction() {
+  for (Parray::iterator it = terms_.begin(); it != terms_.end(); ++it)
+    delete *it;
+}
+
 /** Add a term to the potential function. */
 int PotentialFunction::AddTerm(PotentialTerm::Type typeIn, MdOpts const& opts) {
   PotentialTerm* term = 0;
diff --git a/src/PotentialFunction.h b/src/PotentialFunction.h
index 57b406e909..f187a85229 100644
--- a/src/PotentialFunction.h
+++ b/src/PotentialFunction.h
@@ -12,7 +12,10 @@ class MdOpts;
 /// Hold terms for additive potential.
 class PotentialFunction {
   public:
+    /// CONSTRUCTOR
     PotentialFunction() : current_(0), deg_of_freedom_(0) {}
+    /// DESTRUCTOR
+    ~PotentialFunction();
     /// Add term to function with given options
     int AddTerm(PotentialTerm::Type, MdOpts const&);
     /// Add term to function with default options
diff --git a/src/Structure/BuildAtom.h b/src/Structure/BuildAtom.h
new file mode 100644
index 0000000000..1515d2ce9f
--- /dev/null
+++ b/src/Structure/BuildAtom.h
@@ -0,0 +1,29 @@
+#ifndef INC_STRUCTURE_BUILDATOM_H
+#define INC_STRUCTURE_BUILDATOM_H
+#include "StructureEnum.h"
+namespace Cpptraj {
+namespace Structure {
+/// Hold information for an atom used when building/modelling new coordinates.
+class BuildAtom {
+  public:
+    BuildAtom() : ctype_(IS_UNKNOWN_CHIRALITY) {}
+    /// Set chirality
+    void SetChirality(ChiralType c) { ctype_ = c; }
+    /// Set size of priority array based on number of bonds
+    //void SetNbonds(int n) { priority_.assign(n, -1); }
+    /// \return Pointer to priority array
+    //int* PriorityPtr() { return &(priority_[0]); }
+    /// Used to modify the priority array
+    std::vector<int>& ModifyPriority() { return priority_; }
+
+    /// \return Atom chirality
+    ChiralType Chirality() const { return ctype_; }
+    /// \return Priority array
+    std::vector<int> const& Priority() const { return priority_; }
+  private:
+    ChiralType ctype_;          ///< Chirality around atom
+    std::vector<int> priority_; ///< Indices of bonded atoms, sorted by priority
+};
+}
+}
+#endif
diff --git a/src/Structure/Builder.cpp b/src/Structure/Builder.cpp
new file mode 100644
index 0000000000..4b09556d77
--- /dev/null
+++ b/src/Structure/Builder.cpp
@@ -0,0 +1,109 @@
+#include "Builder.h"
+#include "BuildAtom.h"
+#include "Chirality.h"
+#include "Zmatrix.h"
+#include "../CpptrajStdio.h"
+#include "../Frame.h"
+#include "../Topology.h"
+#include <algorithm> // std::copy
+
+using namespace Cpptraj::Structure;
+
+/** CONSTRUCTOR */
+Builder::Builder() :
+  debug_(0)
+{}
+
+/** Combine two units. Fragment 1 will be merged into Fragment 0 and bonded. */
+int Builder::Combine(Topology&       frag0Top, Frame&       frag0frm,
+                     Topology const& frag1Top, Frame const& frag1frm,
+                     int bondAt0, int bondAt1)
+{
+  int natom0 = frag0Top.Natom();
+  int newNatom = natom0 + frag1Top.Natom();
+
+  // Determine which "direction" we will be combining the fragments.
+  // Make atA belong to the smaller fragment. atB fragment will be "known".
+  // Ensure atB index is what it will be after fragments are combined.
+  Barray posKnown( newNatom, false );
+  int atA, atB;
+  if (frag0Top.HeavyAtomCount() < frag1Top.HeavyAtomCount()) {
+    // Fragment 1 is larger
+    atA = bondAt0;
+    atB = bondAt1 + natom0;
+    for (int at = frag0Top.Natom(); at != newNatom; at++)
+      posKnown[at] = true;
+  } else {
+    // Fragment 0 is larger or equal
+    atA = bondAt1 + natom0;
+    atB = bondAt0;
+    for (int at = 0; at != natom0; at++)
+     posKnown[at] = true;
+  }
+
+  // Combine fragment1 into fragment 0 topology
+  Topology& combinedTop = frag0Top;
+  combinedTop.AppendTop( frag1Top );
+  // Combined fragment1 into fragment 0 coords.
+  // Need to save the original coords in frame0 since SetupFrameV does not preserve.
+  double* tmpcrd0 = new double[natom0*3];
+  std::copy( frag0frm.xAddress(), frag0frm.xAddress()+frag0frm.size(), tmpcrd0 );
+  frag0frm.SetupFrameV( combinedTop.Atoms(), CoordinateInfo(frag0frm.BoxCrd(), false, false, false));
+  std::copy( tmpcrd0, tmpcrd0+natom0*3, frag0frm.xAddress() );
+  std::copy( frag1frm.xAddress(), frag1frm.xAddress()+frag1frm.size(), frag0frm.xAddress()+natom0*3 );
+  Frame& CombinedFrame = frag0frm;
+  delete[] tmpcrd0;
+
+  int chiralityDebug;
+  if (debug_ < 1)
+    chiralityDebug = 0;
+  else
+    chiralityDebug = debug_ - 1;
+  // Get the chirality around each atom before the bond is added.
+  BuildAtom AtomA;
+  if (combinedTop[atA].Nbonds() > 2)
+    AtomA.SetChirality( DetermineChirality(atA, combinedTop, CombinedFrame, chiralityDebug) );
+  if (debug_ > 0)
+    mprintf("DEBUG:\tAtom %4s chirality %6s\n", combinedTop.AtomMaskName(atA).c_str(), chiralStr(AtomA.Chirality()));
+  BuildAtom AtomB;
+  if (combinedTop[atB].Nbonds() > 2)
+    AtomB.SetChirality( DetermineChirality(atB, combinedTop, CombinedFrame, chiralityDebug) );
+  if (debug_ > 0)
+    mprintf("DEBUG:\tAtom %4s chirality %6s\n", combinedTop.AtomMaskName(atB).c_str(), chiralStr(AtomB.Chirality()));
+
+  // Create the bond
+  if (debug_ > 0)
+    mprintf("DEBUG: Bonding atom %s to %s\n", combinedTop.AtomMaskName(atA).c_str(), combinedTop.AtomMaskName(atB).c_str());
+  combinedTop.AddBond( atA, atB ); // TODO pseudo-parameter?
+  // // Regenerate the molecule info FIXME should Topology just do this?
+  if (combinedTop.DetermineMolecules()) return 1;
+
+  // Determine priorities
+  if (combinedTop[atA].Nbonds() > 2) {
+    //AtomA.SetNbonds(combinedTop[atA].Nbonds());
+    SetPriority(AtomA.ModifyPriority(), atA, combinedTop, CombinedFrame, chiralityDebug);
+  }
+  if (combinedTop[atB].Nbonds() > 2) {
+    //AtomB.SetNbonds(combinedTop[atB].Nbonds());
+    SetPriority(AtomB.ModifyPriority(), atB, combinedTop, CombinedFrame, chiralityDebug);
+  }
+
+  // Generate Zmatrix only for ICs involving bonded atoms
+  Zmatrix bondZmatrix;
+
+  bondZmatrix.SetDebug( debug_ );
+  if (bondZmatrix.SetupICsAroundBond(atA, atB, CombinedFrame, combinedTop, posKnown, AtomA, AtomB)) {
+    mprinterr("Error: Zmatrix setup for ICs around %s and %s failed.\n",
+              combinedTop.AtomMaskName(atA).c_str(),
+              combinedTop.AtomMaskName(atB).c_str());
+    return 1;
+  }
+  if (debug_ > 0)
+    bondZmatrix.print(&combinedTop);
+  if (bondZmatrix.SetToFrame( CombinedFrame, posKnown )) {
+    mprinterr("Error: Conversion from bondZmatrix to Cartesian coords failed.\n");
+    return 1;
+  }
+
+  return 0;
+}
diff --git a/src/Structure/Builder.h b/src/Structure/Builder.h
new file mode 100644
index 0000000000..86087d0bec
--- /dev/null
+++ b/src/Structure/Builder.h
@@ -0,0 +1,24 @@
+#ifndef INC_STRUCTURE_BUILDER_H
+#define INC_STRUCTURE_BUILDER_H
+#include <vector>
+class Topology;
+class Frame;
+namespace Cpptraj {
+namespace Structure {
+/// Used to attach different topology/frame combos using internal coordinates
+class Builder {
+  public:
+    /// CONSTRUCTOR
+    Builder();
+    /// Combine second fragment into first fragment and bond
+    int Combine(Topology&, Frame&, Topology const&, Frame const&, int, int);
+    /// Set debug
+    void SetDebug(int d) { debug_ = d; }
+  private:
+    typedef std::vector<bool> Barray;
+
+    int debug_;
+};
+}
+}
+#endif
diff --git a/src/Structure/CMakeLists.txt b/src/Structure/CMakeLists.txt
index b030fd7346..88701e311c 100644
--- a/src/Structure/CMakeLists.txt
+++ b/src/Structure/CMakeLists.txt
@@ -1,12 +1,18 @@
 #CMake buildfile for CPPTRAJ Structure subdirectory.
 target_sources(cpptraj_common_obj PRIVATE
+  ${CMAKE_CURRENT_LIST_DIR}/Builder.cpp
+  ${CMAKE_CURRENT_LIST_DIR}/Chirality.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Disulfide.cpp
   ${CMAKE_CURRENT_LIST_DIR}/FunctionalGroup.cpp
   ${CMAKE_CURRENT_LIST_DIR}/FxnGroupBuilder.cpp
   ${CMAKE_CURRENT_LIST_DIR}/HisProt.cpp
+  ${CMAKE_CURRENT_LIST_DIR}/InternalCoords.cpp
+  ${CMAKE_CURRENT_LIST_DIR}/Model.cpp
+  ${CMAKE_CURRENT_LIST_DIR}/StructureEnum.cpp
   ${CMAKE_CURRENT_LIST_DIR}/StructureRoutines.cpp
   ${CMAKE_CURRENT_LIST_DIR}/SugarBuilder.cpp
   ${CMAKE_CURRENT_LIST_DIR}/Sugar.cpp
   ${CMAKE_CURRENT_LIST_DIR}/SugarLinkAtoms.cpp
   ${CMAKE_CURRENT_LIST_DIR}/SugarToken.cpp
+  ${CMAKE_CURRENT_LIST_DIR}/Zmatrix.cpp
 )
diff --git a/src/Chirality.cpp b/src/Structure/Chirality.cpp
similarity index 79%
rename from src/Chirality.cpp
rename to src/Structure/Chirality.cpp
index 4c44a23fac..c7da6d0b62 100644
--- a/src/Chirality.cpp
+++ b/src/Structure/Chirality.cpp
@@ -1,14 +1,12 @@
 #include "Chirality.h"
-#include "Constants.h"
-#include "CpptrajStdio.h"
-#include "Frame.h"
-#include "Topology.h"
-#include "TorsionRoutines.h"
+#include "../Constants.h"
+#include "../CpptrajStdio.h"
+#include "../Frame.h"
+#include "../Topology.h"
+#include "../TorsionRoutines.h"
 #include <vector>
 #include <algorithm> // sort
 
-using namespace Cpptraj;
-
 /// \return Total priority (i.e. sum of atomic numbers) of atoms bonded to given atom.
 static int totalPriority(Topology const& topIn, int atnum, int rnum,
                          int depth, int tgtdepth, std::vector<bool>& Visited)
@@ -78,16 +76,18 @@ class priority_element {
   *   1-2-3-0
   * where 0 is the chiral center. Negative is S, positive is R.
   */
-Chirality::ChiralType Chirality::DetermineChirality(double& tors, int atnum,
-                                                    Topology const& topIn,
-                                                    Frame const& frameIn, int debugIn)
+Cpptraj::Structure::ChiralType
+  Cpptraj::Structure::DetermineChirality(double& tors, int* AtomIndices,
+                                         int atnum,
+                                         Topology const& topIn,
+                                         Frame const& frameIn, int debugIn)
 {
   tors = 0.0;
   Atom const& atom = topIn[atnum];
   if (atom.Nbonds() < 3) {
     mprinterr("Error: CalcChiralAtomTorsion called for atom %s with less than 3 bonds.\n",
               topIn.AtomMaskName(atnum).c_str());
-    return ERR;
+    return CHIRALITY_ERR;
   }
   // Calculate a priority score for each bonded atom.
   // First just use the atomic number.
@@ -100,6 +100,7 @@ Chirality::ChiralType Chirality::DetermineChirality(double& tors, int atnum,
       mprintf("DEBUG:\t\t%i Priority for %s is %i\n", idx, topIn.AtomMaskName(atom.Bond(idx)).c_str(), priority.back().Priority1());
   }
   // For any identical priorities, need to check who they are bonded to.
+  bool depth_limit_hit = false;
   for (int idx1 = 0; idx1 != atom.Nbonds(); idx1++) {
     for (int idx2 = idx1+1; idx2 != atom.Nbonds(); idx2++) {
       if (priority[idx1] == priority[idx2]) {
@@ -124,9 +125,10 @@ Chirality::ChiralType Chirality::DetermineChirality(double& tors, int atnum,
             break;
           }
           if (depth == 10) {
-            mprinterr("Error: Could not determine priority around '%s'\n",
+            mprintf("Warning: Could not determine priority around '%s'\n",
                       topIn.AtomMaskName(atnum).c_str());
-            return ERR;
+            depth_limit_hit = true;
+            break;
           }
           depth++;
         } // END while identical priorities
@@ -142,6 +144,12 @@ Chirality::ChiralType Chirality::DetermineChirality(double& tors, int atnum,
     mprintf("\n");
   }
 
+  if (AtomIndices != 0) {
+    for (unsigned int ip = 0; ip != priority.size(); ++ip)
+      AtomIndices[ip] = priority[ip].AtNum();
+  }
+  if (depth_limit_hit) return IS_UNKNOWN_CHIRALITY;
+
   tors = Torsion( frameIn.XYZ(priority[0].AtNum()),
                   frameIn.XYZ(priority[1].AtNum()),
                   frameIn.XYZ(priority[2].AtNum()),
@@ -160,10 +168,22 @@ Chirality::ChiralType Chirality::DetermineChirality(double& tors, int atnum,
 }
 
 /** Determine chirality around specified atom. */
-Chirality::ChiralType Chirality::DetermineChirality(int atnum,
-                                                    Topology const& topIn,
-                                                    Frame const& frameIn, int debugIn)
+Cpptraj::Structure::ChiralType
+  Cpptraj::Structure::DetermineChirality(int atnum,
+                                         Topology const& topIn,
+                                         Frame const& frameIn, int debugIn)
+{
+  double tors;
+  return DetermineChirality(tors, 0, atnum, topIn, frameIn, debugIn);
+}
+
+/** Set priority around a specified atom. */
+Cpptraj::Structure::ChiralType
+  Cpptraj::Structure::SetPriority(std::vector<int>& priority,
+                                  int atnum, Topology const& topIn,
+                                  Frame const& frameIn, int debugIn)
 {
+  priority.resize( topIn[atnum].Nbonds() );
   double tors;
-  return DetermineChirality(tors, atnum, topIn, frameIn, debugIn);
+  return DetermineChirality(tors, &priority[0], atnum, topIn, frameIn, debugIn);
 }
diff --git a/src/Structure/Chirality.h b/src/Structure/Chirality.h
new file mode 100644
index 0000000000..e895352409
--- /dev/null
+++ b/src/Structure/Chirality.h
@@ -0,0 +1,18 @@
+#ifndef INC_STRUCTURE_CHIRALITY_H
+#define INC_STRUCTURE_CHIRALITY_H
+#include <vector>
+#include "StructureEnum.h"
+class Topology;
+class Frame;
+namespace Cpptraj {
+namespace Structure {
+
+/// \return Chirality at specified atom, set torsion value
+ChiralType DetermineChirality(double&, int*, int, Topology const&, Frame const&, int);
+/// \return Chirality at specified atom
+ChiralType DetermineChirality(int, Topology const&, Frame const&, int);
+/// \return Chirality at specified atom, set priority
+ChiralType SetPriority(std::vector<int>&, int, Topology const&, Frame const&, int);
+}
+}
+#endif
diff --git a/src/Structure/InternalCoords.cpp b/src/Structure/InternalCoords.cpp
new file mode 100644
index 0000000000..3161f023c7
--- /dev/null
+++ b/src/Structure/InternalCoords.cpp
@@ -0,0 +1,69 @@
+#include <algorithm>
+#include "InternalCoords.h"
+#include "../Topology.h"
+#include "../CpptrajStdio.h"
+
+using namespace Cpptraj::Structure;
+
+const int InternalCoords::NO_ATOM = -1;
+
+/** CONSTRUCTOR */
+InternalCoords::InternalCoords() : 
+  ati_(NO_ATOM)
+{
+  std::fill(idx_, idx_+3, NO_ATOM);
+  std::fill(val_, val_+3, 0);
+}
+
+/** CONSTRUCTOR - Take indices and values */
+InternalCoords::InternalCoords(int atI, int atJ, int atK, int atL,
+                               double dist, double theta, double phi) :
+  ati_(atI)
+{
+  if (ati_ < 0)
+    ati_ = NO_ATOM;
+  if (atJ < 0)
+    idx_[0] = NO_ATOM;
+  else
+    idx_[0] = atJ;
+  if (atK < 0)
+    idx_[1] = NO_ATOM;
+  else
+    idx_[1] = atK;
+  if (atL < 0)
+    idx_[2] = NO_ATOM;
+  else
+    idx_[2] = atL;
+
+  val_[0] = dist;
+  val_[1] = theta;
+  val_[2] = phi;
+}
+
+/** COPY CONSTRUCTOR */
+InternalCoords::InternalCoords(InternalCoords const& rhs) :
+  ati_(rhs.ati_)
+{
+  std::copy( rhs.idx_, rhs.idx_+3, idx_ );
+  std::copy( rhs.val_, rhs.val_+3, val_ );
+}
+
+/** ASSIGNMENT */
+InternalCoords& InternalCoords::operator=(InternalCoords const& rhs) {
+  if (&rhs == this) return *this;
+  ati_ = rhs.ati_;
+  std::copy( rhs.idx_, rhs.idx_+3, idx_ );
+  std::copy( rhs.val_, rhs.val_+3, val_ );
+  return *this;
+}
+
+/** Print to stdout */
+void InternalCoords::printIC(Topology const& top) const {
+  mprintf(" %6i %6i %6i %6i [%s - %s - %s - %s] r=%g t=%g p=%g\n",
+          AtI()+1, AtJ()+1, AtK()+1, AtL()+1,
+          top.AtomMaskName(AtI()).c_str(),
+          top.AtomMaskName(AtJ()).c_str(),
+          top.AtomMaskName(AtK()).c_str(),
+          top.AtomMaskName(AtL()).c_str(),
+          val_[0], val_[1], val_[2]);
+}
diff --git a/src/Structure/InternalCoords.h b/src/Structure/InternalCoords.h
new file mode 100644
index 0000000000..3be154e9d8
--- /dev/null
+++ b/src/Structure/InternalCoords.h
@@ -0,0 +1,48 @@
+#ifndef INC_STRUCTURE_INTERNALCOORDS_H
+#define INC_STRUCTURE_INTERNALCOORDS_H
+class Topology;
+namespace Cpptraj {
+namespace Structure {
+/// Hold internal coordinates for an atom
+/** Given that this is atom i connected to atoms j, k, and l:
+  *   k - j
+  *  /     \
+  * l       i
+  * hold the following:
+  *   distance j - i
+  *   angle    k - j - i
+  *   torsion  l - k - j - i
+  */
+class InternalCoords {
+  public:
+    /// CONSTRUCTOR
+    InternalCoords();
+    /// CONSTRUCTOR - Take atoms i, j, k, l and values dist, theta, phi
+    InternalCoords(int, int, int, int, double, double, double);
+    /// COPY CONSTRUCTOR
+    InternalCoords(InternalCoords const&);
+    /// ASSIGNMENT
+    InternalCoords& operator=(InternalCoords const&);
+
+    static const int NO_ATOM;
+
+    double Dist() const { return val_[0]; }
+    double Theta() const { return val_[1]; }
+    double Phi() const { return val_[2]; }
+
+    int AtI() const { return ati_; }
+    int AtJ() const { return idx_[0]; }
+    int AtK() const { return idx_[1]; }
+    int AtL() const { return idx_[2]; }
+
+    static unsigned int sizeInBytes() { return (4*sizeof(int)) + (3*sizeof(double)); }
+
+    void printIC(Topology const&) const;
+  private:
+    int ati_;       ///< Atom I index
+    int idx_[3];    ///< Atom indices for distance, angle, torsion
+    double val_[3]; ///< Values for distance, angle, torsion
+};
+}
+}
+#endif
diff --git a/src/Structure/Model.cpp b/src/Structure/Model.cpp
new file mode 100644
index 0000000000..affbf21f06
--- /dev/null
+++ b/src/Structure/Model.cpp
@@ -0,0 +1,258 @@
+#include "Model.h"
+#include "BuildAtom.h"
+#include "../CpptrajStdio.h"
+#include "../Topology.h"
+#include "../TorsionRoutines.h"
+#include "../Constants.h"
+
+/** Attempt to assign a reasonable value for theta internal coordinate for
+  * atom i given that atoms j and k have known positions.
+  */
+int Cpptraj::Structure::Model::AssignTheta(double& theta, int ai, int aj, int ak, Topology const& topIn, Frame const& frameIn, std::vector<bool> const& atomPositionKnown, int debug)
+{
+  // Figure out hybridization and chirality of atom j.
+  if (debug > 0)
+    mprintf("DEBUG: AssignTheta for atom j : %s\n", topIn.AtomMaskName(aj).c_str());
+
+  enum HybridizationType { SP = 0, SP2, SP3, UNKNOWN_HYBRIDIZATION };
+
+  Atom const& AJ = topIn[aj];
+  if (debug > 0) {
+    mprintf("DEBUG:\t\tI %s Nbonds: %i\n", topIn[ai].ElementName(), topIn[ai].Nbonds());
+    mprintf("DEBUG:\t\tJ %s Nbonds: %i\n", AJ.ElementName(), AJ.Nbonds());
+    mprintf("DEBUG:\t\tK %s Nbonds: %i\n", topIn[ak].ElementName(), topIn[ak].Nbonds());
+  }
+  // Sanity check
+  if (AJ.Nbonds() < 2) {
+    mprinterr("Internal Error: AssignTheta() called for atom J %s with fewer than 2 bonds.\n", topIn.AtomMaskName(aj).c_str());
+    return 1;
+  }
+
+  HybridizationType hybrid = UNKNOWN_HYBRIDIZATION;
+  // Handle specific elements
+  switch (AJ.Element()) {
+    case Atom::CARBON :
+      switch (AJ.Nbonds()) {
+        case 2 : hybrid = SP; break;
+        case 3 : hybrid = SP2; break;
+        case 4 : hybrid = SP3; break;
+      }
+      break;
+    case Atom::NITROGEN :
+      switch (AJ.Nbonds()) {
+        case 2 : hybrid = SP2; break;
+        case 3 :
+          // Check for potential SP2. If only 1 of the bonded atoms is
+          // hydrogen, assume SP2. TODO actually check for aromaticity.
+          int n_hydrogens = 0;
+          for (Atom::bond_iterator bat = AJ.bondbegin(); bat != AJ.bondend(); ++bat)
+            if (topIn[*bat].Element() == Atom::HYDROGEN)
+              n_hydrogens++;
+          if (n_hydrogens == 1)
+            hybrid = SP2;
+          else
+            hybrid = SP3;
+          break;
+      }
+      break;
+    case Atom::OXYGEN :
+      switch (AJ.Nbonds()) {
+        case 2 : hybrid = SP3; break;
+      }
+      break;
+    case Atom::SULFUR :
+      switch (AJ.Nbonds()) {
+        case 2 : hybrid = SP3; break;
+      }
+      break;
+    default: hybrid = UNKNOWN_HYBRIDIZATION; break;
+  }
+  // Fill in what values we can for known atoms
+/*  std::vector<double> knownTheta( AJ.Nbonds() );
+  int knownIdx = -1;
+  for (int idx = 0; idx < AJ.Nbonds(); idx++) {
+    int atnum = AJ.Bond(idx);
+    if (atnum != ak && atomPositionKnown[atnum]) {
+      knownTheta[idx] = CalcAngle(frameIn.XYZ(atnum),
+                                  frameIn.XYZ(aj),
+                                  frameIn.XYZ(ak));
+      mprintf("DEBUG:\t\tKnown theta for %s = %g\n", topIn.AtomMaskName(atnum).c_str(), knownTheta[idx]*Constants::RADDEG);
+      if (knownIdx == -1) knownIdx = idx; // FIXME handle more than 1 known
+    }
+  }
+  if (knownIdx == -1) {*/
+    //mprintf("DEBUG:\t\tNo known theta.\n");
+  if (hybrid == UNKNOWN_HYBRIDIZATION) {
+    // Assign a theta based on number of bonds 
+    switch (AJ.Nbonds()) {
+      case 4 : hybrid = SP3; break;
+      case 3 : hybrid = SP2; break;
+      case 2 : hybrid = SP; break;
+      default : mprinterr("Internal Error: AssignTheta(): Unhandled # bonds for %s (%i)\n", topIn.AtomMaskName(aj).c_str(), AJ.Nbonds()); return 1;
+    }
+  }
+  // Assign a theta based on hybridization
+  switch (hybrid) {
+    case SP3 : theta = 109.5 * Constants::DEGRAD; break;
+    case SP2 : theta = 120.0 * Constants::DEGRAD; break;
+    case SP  : theta = 180.0 * Constants::DEGRAD; break;
+    default : mprinterr("Internal Error: AssignTheta(): Unhandled hybridization for %s (%i)\n", topIn.AtomMaskName(aj).c_str(), AJ.Nbonds()); return 1;
+  }/*
+  } else {
+    theta = knownTheta[knownIdx]; // TODO just use above guess via hybrid?
+  }*/
+
+  return 0;
+}
+
+/// Recursive function to return depth from an atom along bonds
+static int atom_depth(int& depth,
+                      int at, Topology const& topIn, std::vector<bool>& visited, int maxdepth)
+{
+  if (depth == maxdepth) return 0;
+  depth++;
+  visited[at] = true;
+  int depthFromHere = 1;
+  for (Atom::bond_iterator bat = topIn[at].bondbegin(); bat != topIn[at].bondend(); ++bat)
+  {
+    if (!visited[*bat])
+      depthFromHere += atom_depth( depth, *bat, topIn, visited, maxdepth );
+  }
+  return depthFromHere;
+}
+
+static inline double wrap360(double phi) {
+  if (phi > Constants::PI)
+    return phi - Constants::TWOPI;
+  else if (phi < -Constants::PI)
+    return phi + Constants::TWOPI;
+  else
+    return phi;
+}
+
+/** Attempt to assign a reasonable value for phi internal coordinate for atom i
+  * given that atoms j k and l have known positions.
+  *   j - k
+  *  /     \
+  * i       l
+  */
+int Cpptraj::Structure::Model::AssignPhi(double& phi, int ai, int aj, int ak, int al,
+                                         Topology const& topIn, Frame const& frameIn,
+                                         std::vector<bool> const& atomPositionKnown,
+                                         BuildAtom const& AtomJ, int debug)
+{
+  // Figure out hybridization and chirality of atom j.
+  if (debug > 0)
+    mprintf("DEBUG: AssignPhi for atom j : %s\n", topIn.AtomMaskName(aj).c_str());
+
+  Atom const& AJ = topIn[aj];
+  if (debug > 0) mprintf("DEBUG:\t\tNbonds: %i\n", AJ.Nbonds());
+  // If atom J only has 2 bonds, ai-aj-ak-al is the only possibility.
+  if (AJ.Nbonds() < 3) {
+    if (debug > 0)
+      mprintf("DEBUG:\t\tFewer than 3 bonds. Setting phi to -180.\n");
+    phi = -180 * Constants::DEGRAD;
+    return 0;
+  }
+
+  // TODO check that atom i actually ends up on the list?
+  std::vector<int> const& priority = AtomJ.Priority();
+  if (debug > 0) {
+    mprintf("DEBUG: Original chirality around J %s is %s\n", topIn.AtomMaskName(aj).c_str(), chiralStr(AtomJ.Chirality()));
+    mprintf("DEBUG:\t\tPriority around J %s(%i):", 
+            topIn.AtomMaskName(aj).c_str(), (int)atomPositionKnown[aj]);
+    for (int idx = 0; idx < AJ.Nbonds(); idx++)
+      mprintf(" %s(%i)", topIn.AtomMaskName(priority[idx]).c_str(), (int)atomPositionKnown[priority[idx]]);
+    mprintf("\n");
+  }
+
+  // Fill in what values we can for known atoms
+  std::vector<double> knownPhi( AJ.Nbonds() );
+  int knownIdx = -1;
+  for (int idx = 0; idx < AJ.Nbonds(); idx++) {
+    int atnum = priority[idx];
+    if (atnum != ak && atomPositionKnown[atnum] &&
+                       atomPositionKnown[aj] &&
+                       atomPositionKnown[ak] &&
+                       atomPositionKnown[al])
+    {
+      knownPhi[idx] = Torsion(frameIn.XYZ(atnum),
+                              frameIn.XYZ(aj),
+                              frameIn.XYZ(ak),
+                              frameIn.XYZ(al));
+      if (debug > 0)
+        mprintf("DEBUG:\t\tKnown phi for %s = %g\n", topIn.AtomMaskName(atnum).c_str(), knownPhi[idx]*Constants::RADDEG);
+      if (knownIdx == -1) knownIdx = idx; // FIXME handle more than 1 known
+    }
+  }
+
+  // If we have to assign an initial phi, make trans the longer branch
+  if (knownIdx == -1) {
+    std::vector<bool> visited = atomPositionKnown;
+    // TODO: Ensure bonded atoms are not yet visited?
+    visited[aj] = true;
+    visited[ak] = true;
+    std::vector<int> depth( AJ.Nbonds() );
+    for (int idx = 0; idx < AJ.Nbonds(); idx++) {
+      int atnum = priority[idx];
+      if (atnum != ak) {
+        int currentDepth = 0;
+        depth[idx] = atom_depth(currentDepth, atnum, topIn, visited, 10);
+        if (debug > 0)
+          mprintf("DEBUG:\t\tAJ %s depth from %s is %i\n",
+                  topIn.AtomMaskName(aj).c_str(), topIn.AtomMaskName(atnum).c_str(), depth[idx]);
+        if (knownIdx == -1 && depth[idx] < 3) {
+          knownIdx = idx;
+          knownPhi[idx] = 0;
+        }
+      }
+    }
+  }
+
+  // The interval will be 360 / (number of bonds - 1)
+  double interval = Constants::TWOPI / (AJ.Nbonds() - 1);
+
+  double startPhi;
+  if (knownIdx == -1) {
+    startPhi = -180*Constants::DEGRAD;
+    if (debug > 0) mprintf("DEBUG:\t\tNo known phi. Setting to %g.\n", startPhi*Constants::RADDEG);
+    knownIdx = 0;
+  } else
+    startPhi = knownPhi[knownIdx];
+
+  if (AtomJ.Chirality() == IS_R) {
+    startPhi = -startPhi;
+    interval = -interval;
+  }
+  if (debug > 0) {
+    mprintf("DEBUG:\t\tStart phi is %g degrees\n", startPhi*Constants::RADDEG);
+    mprintf("DEBUG:\t\tInterval is %g degrees\n", interval * Constants::RADDEG);
+  }
+    
+  // Forward direction
+  double currentPhi = startPhi;
+  for (int idx = knownIdx; idx < AJ.Nbonds(); idx++) {
+    int atnum = priority[idx];
+    if (atnum != ak) {
+      if (atnum == ai) phi = currentPhi;
+      if (debug > 0)
+        mprintf("DEBUG:\t\t\t%s phi= %g\n", topIn.AtomMaskName(atnum).c_str(), currentPhi*Constants::RADDEG);
+      currentPhi += interval;
+      currentPhi = wrap360(currentPhi);
+    }
+  }
+  // Reverse direction
+  currentPhi = startPhi - interval;
+  for (int idx = knownIdx - 1; idx > -1; idx--) {
+    int atnum = priority[idx];
+    if (atnum != ak) {
+      if (atnum == ai) phi = currentPhi;
+      if (debug > 0)
+        mprintf("DEBUG:\t\t\t%s phi= %g\n", topIn.AtomMaskName(atnum).c_str(), currentPhi*Constants::RADDEG);
+      currentPhi -= interval;
+      currentPhi = wrap360(currentPhi);
+    }
+  }
+
+  return 0;
+}
diff --git a/src/Structure/Model.h b/src/Structure/Model.h
new file mode 100644
index 0000000000..240e64875e
--- /dev/null
+++ b/src/Structure/Model.h
@@ -0,0 +1,20 @@
+#ifndef INC_STRUCTURE_MODEL_H
+#define INC_STRUCTURE_MODEL_H
+#include <vector>
+#include "StructureEnum.h"
+class Topology;
+class Frame;
+namespace Cpptraj {
+namespace Structure {
+class BuildAtom;
+/// Routines to generate model parameters
+namespace Model {
+/// Given atoms J K and L, attempt to assign a reasonable value for phi for atom I
+int AssignPhi(double&, int, int, int, int, Topology const&, Frame const&, std::vector<bool> const&, BuildAtom const&, int);
+/// Given atoms J and K, attempt to assign a reasonable value for theta for atom I
+int AssignTheta(double&, int, int, int, Topology const&, Frame const&, std::vector<bool> const&, int);
+
+} // END namespace Model
+} // END namespace Structure
+} // END namespace Cpptraj
+#endif
diff --git a/src/Structure/StructureEnum.cpp b/src/Structure/StructureEnum.cpp
new file mode 100644
index 0000000000..1ef86d24f8
--- /dev/null
+++ b/src/Structure/StructureEnum.cpp
@@ -0,0 +1,12 @@
+#include "StructureEnum.h"
+
+/** \return string corresponding to ChiralType */
+const char* Cpptraj::Structure::chiralStr(ChiralType ct) {
+  switch (ct) {
+    case CHIRALITY_ERR : return "Error";
+    case IS_S : return "S";
+    case IS_R : return "R";
+    case IS_UNKNOWN_CHIRALITY : return "Unknown";
+  }
+  return 0;
+}
diff --git a/src/Structure/StructureEnum.h b/src/Structure/StructureEnum.h
new file mode 100644
index 0000000000..311767921a
--- /dev/null
+++ b/src/Structure/StructureEnum.h
@@ -0,0 +1,12 @@
+#ifndef INC_STRUCTURE_STRUCTUREENUM_H
+#define INC_STRUCTURE_STRUCTUREENUM_H
+namespace Cpptraj {
+namespace Structure {
+
+enum ChiralType { CHIRALITY_ERR = 0, IS_S, IS_R, IS_UNKNOWN_CHIRALITY };
+/// \return String corresponding to ChiralType
+const char* chiralStr(ChiralType);
+
+}
+}
+#endif
diff --git a/src/Structure/SugarBuilder.cpp b/src/Structure/SugarBuilder.cpp
index 7322bf9ded..1d805996cb 100644
--- a/src/Structure/SugarBuilder.cpp
+++ b/src/Structure/SugarBuilder.cpp
@@ -1,4 +1,5 @@
 #include "SugarBuilder.h"
+#include "Chirality.h"
 #include "FxnGroupBuilder.h"
 #include "ResStatArray.h"
 #include "StructureRoutines.h"
@@ -6,7 +7,6 @@
 #include "SugarLinkAtoms.h"
 #include "../ArgList.h"
 #include "../CharMask.h" // for linkage determination
-#include "../Chirality.h"
 #include "../CpptrajFile.h"
 #include "../CpptrajStdio.h"
 #include "../DistRoutines.h"
@@ -1113,22 +1113,18 @@ const
     cdebug = 1;
   else
     cdebug = 0;
-  Cpptraj::Chirality::ChiralType ctypeR = Cpptraj::Chirality::
-                                          DetermineChirality(sugar.HighestStereocenter(),
-                                                             topIn, frameIn, cdebug);
-  if (ctypeR == Cpptraj::Chirality::ERR) {
+  ChiralType ctypeR = DetermineChirality(sugar.HighestStereocenter(), topIn, frameIn, cdebug);
+  if (ctypeR == CHIRALITY_ERR || ctypeR == IS_UNKNOWN_CHIRALITY) {
     mprinterr("Error: Could not determine configuration for furanose.\n"); // TODO warn?
     return 1;
   }
-  if (ctypeR == Cpptraj::Chirality::IS_R)
+  if (ctypeR == IS_R)
     stoken.SetChirality(SugarToken::IS_D);
   else
     stoken.SetChirality(SugarToken::IS_L);
 
-  Cpptraj::Chirality::ChiralType ctypeA = Cpptraj::Chirality::
-                                          DetermineChirality(sugar.AnomericAtom(),
-                                                             topIn, frameIn, cdebug);
-  if (ctypeA == Cpptraj::Chirality::ERR) {
+  ChiralType ctypeA = DetermineChirality(sugar.AnomericAtom(), topIn, frameIn, cdebug);
+  if (ctypeA == CHIRALITY_ERR || ctypeA == IS_UNKNOWN_CHIRALITY) {
     mprinterr("Error: Could not determine chirality around anomeric atom for furanose.\n"); // TODO warn?
     return 1;
   }
diff --git a/src/Structure/Zmatrix.cpp b/src/Structure/Zmatrix.cpp
new file mode 100644
index 0000000000..538564c2b9
--- /dev/null
+++ b/src/Structure/Zmatrix.cpp
@@ -0,0 +1,904 @@
+#include <vector>
+#include <algorithm> // std::sort, std::min, std::max
+#include <stack>
+#include <cmath> // cos
+#include <utility> // std::pair
+#include "Zmatrix.h"
+#include "BuildAtom.h"
+#include "Model.h"
+#include "../Frame.h"
+#include "../CpptrajStdio.h"
+#include "../Constants.h"
+#include "../DistRoutines.h"
+#include "../Topology.h"
+#include "../TorsionRoutines.h"
+
+using namespace Cpptraj::Structure;
+
+/** CONSTRUCTOR */
+Zmatrix::Zmatrix() :
+  debug_(0),
+  icseed0_(InternalCoords::NO_ATOM),
+  icseed1_(InternalCoords::NO_ATOM),
+  icseed2_(InternalCoords::NO_ATOM),
+  seed0Pos_(0.0),
+  seed1Pos_(0.0),
+  seed2Pos_(0.0),
+  seedAt0_(InternalCoords::NO_ATOM),
+  seedAt1_(InternalCoords::NO_ATOM),
+  seedAt2_(InternalCoords::NO_ATOM)
+{}
+
+/** Clear the zmatrix. */
+void Zmatrix::clear() {
+  IC_.clear();
+  icseed0_ = InternalCoords::NO_ATOM;
+  icseed1_ = InternalCoords::NO_ATOM;
+  icseed2_ = InternalCoords::NO_ATOM;
+  seed0Pos_ = Vec3(0.0);
+  seed1Pos_ = Vec3(0.0);
+  seed2Pos_ = Vec3(0.0);
+  seedAt0_ = InternalCoords::NO_ATOM;
+  seedAt1_ = InternalCoords::NO_ATOM;
+  seedAt2_ = InternalCoords::NO_ATOM;
+}
+
+/// Error message for seed already set
+static inline int seed_err(int iseed) {
+  mprinterr("Internal Error: Internal coord seed %i is already set.\n", iseed);
+  return 1;
+}
+
+/** Add internal coords. If any of the atoms are not set assume this is one
+  * of the 3 seed atoms and determine which one.
+  */
+int Zmatrix::AddIC(InternalCoords const& ic) {
+  if (ic.AtJ() == InternalCoords::NO_ATOM &&
+      ic.AtK() == InternalCoords::NO_ATOM &&
+      ic.AtL() == InternalCoords::NO_ATOM)
+  { // Potential seed0
+    if (icseed0_ != InternalCoords::NO_ATOM)
+      return seed_err(0);
+    icseed0_ = IC_.size();
+  } else if (ic.AtK() == InternalCoords::NO_ATOM &&
+             ic.AtL() == InternalCoords::NO_ATOM)
+  { // Potential seed1
+    if (icseed1_ != InternalCoords::NO_ATOM)
+      return seed_err(1);
+    icseed1_ = IC_.size();
+  } else if (ic.AtL() == InternalCoords::NO_ATOM) {
+    // Potential seed2
+    if (icseed2_ != InternalCoords::NO_ATOM)
+      return seed_err(2);
+    icseed2_ = IC_.size();
+  }
+
+  IC_.push_back( ic );
+  return 0;
+}
+
+/** Set IC at specified position. */ // TODO check if seed?
+void Zmatrix::SetIC(unsigned int idx, InternalCoords const& ic) {
+  IC_[idx] = ic;
+}
+
+/** \return Array containing indices of ICs with specified atom i. */
+std::vector<int> Zmatrix::AtomI_indices(int atomi) const {
+  std::vector<int> indices;
+  for (unsigned int idx = 0; idx != IC_.size(); idx++) {
+    if (IC_[idx].AtI() == atomi)
+      indices.push_back( (int)idx );
+  }
+  return indices;
+}
+
+/** Print to stdout */
+void Zmatrix::print(Topology* topIn) const {
+  mprintf("%zu internal coords.\n", IC_.size());
+  mprintf("Seed IC indices    : %i %i %i\n", icseed0_+1, icseed1_+1, icseed2_+1);
+  mprintf("Seed Cart. indices : %i %i %i\n", seedAt0_+1, seedAt1_+1, seedAt2_+1);
+  seed0Pos_.Print("Seed0");
+  seed1Pos_.Print("Seed1");
+  seed2Pos_.Print("Seed2");
+  if (topIn == 0) {
+    mprintf("%-8s %8s %8s %8s %8s %12s %12s %12s\n",
+            "#Idx", "AtI", "AtJ", "AtK", "AtL", "Dist", "Theta", "Phi");
+    for (ICarray::const_iterator it = IC_.begin(); it != IC_.end(); ++it)
+      mprintf("%-8li %8i %8i %8i %8i %12.4f %12.4f %12.4f\n", it - IC_.begin()+1,
+              it->AtI()+1, it->AtJ()+1, it->AtK()+1, it->AtL()+1,
+              it->Dist(), it->Theta(), it->Phi());
+  } else {
+    mprintf("%-6s %6s %8s %6s %8s %6s %8s %6s %8s %6s %6s %6s\n",
+            "#Idx", "AtI", "NmI", "AtJ", "NmJ", "AtK", "NmK", "AtL", "NmL", "Dist", "Theta", "Phi");
+    for (ICarray::const_iterator it = IC_.begin(); it != IC_.end(); ++it)
+      mprintf("%-6li %6i %8s %6i %8s %6i %8s %6i %8s %6.2f %6.2f %6.2f\n", it - IC_.begin()+1,
+              it->AtI()+1, topIn->AtomMaskName(it->AtI()).c_str(),
+              it->AtJ()+1, topIn->AtomMaskName(it->AtJ()).c_str(),
+              it->AtK()+1, topIn->AtomMaskName(it->AtK()).c_str(),
+              it->AtL()+1, topIn->AtomMaskName(it->AtL()).c_str(),
+              it->Dist(), it->Theta(), it->Phi());
+  }
+}
+
+/** \return True if all Cartesian seeds are set. */
+bool Zmatrix::HasCartSeeds() const {
+  bool has_cart_seed = (seedAt0_ != InternalCoords::NO_ATOM &&
+                        seedAt1_ != InternalCoords::NO_ATOM &&
+                        seedAt2_ != InternalCoords::NO_ATOM); 
+  return has_cart_seed;
+}
+
+/** Set seeds from specified atoms. */
+int Zmatrix::SetSeedPositions(Frame const& frameIn, Topology const& topIn, int a1, int a2, int a3)
+{
+  // a1 must be bonded to a2
+  if (!topIn[a1].IsBondedTo(a2)) {
+    mprinterr("Error: In topology '%s', seed 0 atom '%s' is not bonded to seed 1 atom '%s'\n",
+              topIn.c_str(), topIn.AtomMaskName(a1).c_str(), topIn.AtomMaskName(a2).c_str());
+    return 1;
+  }
+  // a2 must be bonded to a3
+  if (!topIn[a2].IsBondedTo(a3)) {
+    mprinterr("Error: In topology '%s', seed 1 atom '%s' is not bonded to seed 2 atom '%s'\n",
+              topIn.c_str(), topIn.AtomMaskName(a2).c_str(), topIn.AtomMaskName(a3).c_str());
+    return 1;
+  }
+  // Store seed positions
+  seedAt0_  = a1;
+  seed0Pos_ = Vec3(frameIn.XYZ(a1));
+  seedAt1_  = a2;
+  seed1Pos_ = Vec3(frameIn.XYZ(a2));
+  seedAt2_  = a3;
+  seed2Pos_ = Vec3(frameIn.XYZ(a3));
+  if (debug_ > 0)
+    mprintf("DEBUG: Seed atoms: %s - %s - %s\n",
+            topIn.AtomMaskName(a1).c_str(),
+            topIn.AtomMaskName(a2).c_str(),
+            topIn.AtomMaskName(a3).c_str());
+
+  return 0;
+}
+
+/// Mark an IC as used, update used count
+static inline void MARK(int i, std::vector<bool>& isUsed, unsigned int& Nused) {
+  if (!isUsed[i]) {
+    isUsed[i] = true;
+    Nused++;
+  }
+}
+
+/** Calculate and add an internal coordinate given atom indices
+  * and corresponding Cartesian coordinates.
+  */
+void Zmatrix::addIc(int at0, int at1, int at2, int at3,
+                   const double* xyz0, const double* xyz1,
+                   const double* xyz2, const double* xyz3)
+{
+  IC_.push_back( InternalCoords(at0, at1, at2, at3,
+                                sqrt(DIST2_NoImage(xyz0, xyz1)),
+                                CalcAngle(xyz0, xyz1, xyz2) * Constants::RADDEG,
+                                Torsion(xyz0, xyz1, xyz2, xyz3) * Constants::RADDEG) );
+}
+
+/** Simple automatic setting of seeds for a molecule.
+  * seed0 - seed1 - seed 2
+  * Prefer that seed1 has only exactly 2 bonds. It cannot have 1.
+  */
+int Zmatrix::autoSetSeeds_simple(Frame const& frameIn, Topology const& topIn, Molecule const& mol)
+{
+  seedAt0_ = InternalCoords::NO_ATOM;
+  seedAt1_ = InternalCoords::NO_ATOM;
+  seedAt2_ = InternalCoords::NO_ATOM;
+
+  // Handle special cases
+  if (mol.NumAtoms() < 1) {
+    mprinterr("Internal Error: Zmatrix::autoSetSeeds_simple() called with an empty molecule.\n");
+    return 1;
+  }
+  if (mol.NumAtoms() == 1) {
+    seedAt0_ = mol.MolUnit().Front();
+    seed0Pos_ = Vec3(frameIn.XYZ(seedAt0_));
+    return 0;
+  } else if (mol.NumAtoms() == 2) {
+    seedAt0_ = mol.MolUnit().Front();
+    seed0Pos_ = Vec3(frameIn.XYZ(seedAt0_));
+    if (topIn[seedAt0_].Nbonds() != 1) {
+      mprinterr("Internal Error: Zmatrix::autoSetSeeds_simple(): 2 atoms but no bonds.\n");
+      return 1;
+    }
+    seedAt1_ = topIn[seedAt0_].Bond(0);
+    seed1Pos_ = Vec3(frameIn.XYZ(seedAt1_));
+    return 0;
+  }
+
+  int potentialSeed1 = -1;
+  int potentialSeedNbonds = -1;
+  for (Unit::const_iterator seg = mol.MolUnit().segBegin();
+                            seg != mol.MolUnit().segEnd(); ++seg)
+  {
+    for (int idx = seg->Begin(); idx != seg->End(); ++idx) {
+      if (topIn[idx].Nbonds() > 1) {
+        // New seed1 if this seed1 has fewer bonds
+        if (potentialSeed1 == -1 || topIn[idx].Nbonds() < potentialSeedNbonds) {
+          potentialSeed1 = idx;
+          potentialSeedNbonds = topIn[idx].Nbonds();
+          if (potentialSeedNbonds == 2) {
+            seedAt1_ = idx;
+            break;
+          }
+        }
+      }
+    } // END loop over segment atoms
+    // Exit if a good seed was found
+    if (seedAt1_ != InternalCoords::NO_ATOM) break;
+  }
+  if (seedAt1_ == InternalCoords::NO_ATOM) {
+    if (debug_ > 0)
+      mprintf("DEBUG: No seed1 with just 2 bonds found. Using seed1 with %i bonds.\n", potentialSeedNbonds);
+    seedAt1_ = potentialSeed1;
+  }
+  if (seedAt1_ == InternalCoords::NO_ATOM) {
+    mprinterr("Error: No seed1 could be found.\n");
+    return 1;
+  }
+
+  // seed0 will be lowest index, seed 1 will be highest
+  int lowestidx = -1;
+  int highestidx = -1;
+  for (Atom::bond_iterator bat = topIn[seedAt1_].bondbegin(); bat != topIn[seedAt1_].bondend(); ++bat)
+  {
+    if (lowestidx == -1) {
+      lowestidx = *bat;
+      highestidx = *bat;
+    } else {
+      lowestidx = std::min(lowestidx, *bat);
+      highestidx = std::max(highestidx, *bat);
+    }
+  }
+  seedAt0_ = lowestidx;
+  seedAt2_ = highestidx;
+
+  if (debug_ > 0) {
+    mprintf("DEBUG: Potential seed 0: %i %s\n", seedAt0_+1, topIn.AtomMaskName(seedAt0_).c_str());
+    mprintf("DEBUG: Potential seed 1: %i %s\n", seedAt1_+1, topIn.AtomMaskName(seedAt1_).c_str());
+    mprintf("DEBUG: Potential seed 2: %i %s\n", seedAt2_+1, topIn.AtomMaskName(seedAt2_).c_str());
+  }
+    
+  seed0Pos_ = Vec3(frameIn.XYZ(seedAt0_));
+  seed1Pos_ = Vec3(frameIn.XYZ(seedAt1_));
+  seed2Pos_ = Vec3(frameIn.XYZ(seedAt2_));
+
+  return 0;
+}
+
+/// For DEBUG, print integer array
+static inline void printIarray(std::vector<int> const& arr, const char* desc, Topology const& topIn) {
+  mprintf("DEBUG:\t\t%s:", desc);
+  for (std::vector<int>::const_iterator it = arr.begin(); it != arr.end(); ++it)
+    //mprintf(" %i", *it);
+    mprintf(" %s", topIn.AtomMaskName(*it).c_str());
+  mprintf("\n");
+}
+
+/// Hold 4 atoms
+class PHI {
+  public:
+    PHI(int ai, int aj, int ak, int al) : ai_(ai), aj_(aj), ak_(ak), al_(al) {}
+    int ai_, aj_, ak_, al_;
+};
+
+/** Trace molecule starting from L - K - J - ??. */
+int Zmatrix::traceMol(int atL0, int atK0, int atJ0,
+                      Frame const& frameIn, Topology const& topIn, unsigned int maxnatom,
+                      unsigned int& nHasIC, Barray& hasIC)
+{
+  // Will hold branches that need to be investigated
+  std::stack<PHI> Branches;
+
+  int atL = atL0;
+  int atK = atK0;
+  int atJ = atJ0;
+
+  //int debug_it = 0; // DEBUG
+  unsigned int maxStack = 0;
+
+  while (nHasIC < maxnatom) {
+    if (debug_ > 1)
+      mprintf("\nDEBUG: nHasIC= %8u / %8u : %s - %s - %s -\n", nHasIC, maxnatom,
+              topIn.AtomMaskName(atL).c_str(),
+              topIn.AtomMaskName(atK).c_str(),
+              topIn.AtomMaskName(atJ).c_str());
+    // List all atoms bonded to J with the following priority:
+    //   1) Atoms with 1 bond.
+    //   2) Low index atoms.
+    Iarray OneBondAtoms; // TODO allocate outside loop?
+    Iarray OtherAtoms;
+    for (Atom::bond_iterator bat = topIn[atJ].bondbegin(); bat != topIn[atJ].bondend(); ++bat)
+    {
+      if (!hasIC[*bat]) {
+        if (topIn[*bat].Nbonds() == 1)
+          OneBondAtoms.push_back( *bat );
+        else if (*bat != atK)
+          OtherAtoms.push_back( *bat );
+      }
+    }
+    if (OtherAtoms.size() > 1)
+      std::sort( OtherAtoms.begin(), OtherAtoms.end() );
+    if (debug_ > 1) {
+      printIarray( OneBondAtoms, "OneBondAtoms", topIn );
+      printIarray( OtherAtoms, "OtherAtoms", topIn );
+    }
+    // Create ICs for 1 bond atoms
+    for (Iarray::const_iterator atI = OneBondAtoms.begin(); atI != OneBondAtoms.end(); ++atI) {
+      addIc(*atI, atJ, atK, atL, frameIn.XYZ(*atI), frameIn.XYZ(atJ), frameIn.XYZ(atK), frameIn.XYZ(atL));
+      if (debug_ > 1) {
+        mprintf("DEBUG: Added (1 atom) ");
+        IC_.back().printIC(topIn);
+      }
+      MARK(*atI, hasIC, nHasIC);
+    }
+    // If nothing else, check the stack
+    if (OtherAtoms.empty()) {
+      // If no branches, done for now.
+      if (Branches.empty()) {
+        if (debug_ > 1)
+          mprintf("DEBUG: No more branches. Exiting traceMol.\n");
+        break;
+      }
+      // Add IC for the branch
+      bool has_next = false;
+      while (!Branches.empty()) {
+        PHI const& p = Branches.top();
+        if (debug_ > 1) {
+          mprintf("DEBUG:\t\tPopped off stack: %s - %s - %s - %s\n",
+                  topIn.AtomMaskName(p.ai_).c_str(),
+                  topIn.AtomMaskName(p.aj_).c_str(),
+                  topIn.AtomMaskName(p.ak_).c_str(),
+                  topIn.AtomMaskName(p.al_).c_str());
+        }
+        if (!hasIC[p.ai_]) {
+          addIc(p.ai_, p.aj_, p.ak_, p.al_, frameIn.XYZ(p.ai_), frameIn.XYZ(p.aj_), frameIn.XYZ(p.ak_), frameIn.XYZ(p.al_));
+          if (debug_ > 1) {
+            mprintf("DEBUG: Added (stack) ");
+            IC_.back().printIC(topIn);
+          }
+          Branches.pop();
+          MARK(p.ai_, hasIC, nHasIC);
+          // Designate branch as next.
+          atL = p.ak_;
+          atK = p.aj_;
+          atJ = p.ai_;
+          has_next = true;
+          break;
+        } else {
+          if (debug_ > 1) {
+            mprintf("DEBUG:\t\t%s already has an IC.\n", topIn.AtomMaskName(p.ai_).c_str());
+            std::vector<int> indices = AtomI_indices(p.ai_);
+            // TODO check empty or size > 1
+            IC_[indices.front()].printIC( topIn );
+          }
+          Branches.pop();
+        }
+      } // END while branches remain on stack
+      if (!has_next) {
+        if (debug_ > 1) mprintf("DEBUG:\t\tNothing left on the stack.\n");
+        break;
+      } 
+    } else {
+      int atI = OtherAtoms.front();
+      if (debug_ > 1) {
+        mprintf("DEBUG:\t\tNext: %s - %s - %s - %s\n",
+                topIn.AtomMaskName(atI).c_str(),
+                topIn.AtomMaskName(atJ).c_str(),
+                topIn.AtomMaskName(atK).c_str(),
+                topIn.AtomMaskName(atL).c_str());
+      }
+      // Add lowest index as IC
+      if (!hasIC[atI]) {
+        addIc(atI, atJ, atK, atL, frameIn.XYZ(atI), frameIn.XYZ(atJ), frameIn.XYZ(atK), frameIn.XYZ(atL));
+        if (debug_ > 1) {
+          mprintf("DEBUG: Added (next) ");
+          IC_.back().printIC(topIn);
+        }
+        MARK(atI, hasIC, nHasIC);
+      }
+      // Place all above lowest index on the stack.
+      for (unsigned int ii = 1; ii < OtherAtoms.size(); ii++) {
+        Branches.push( PHI(OtherAtoms[ii], atJ, atK, atL) );
+        maxStack = std::max(maxStack, (unsigned int)Branches.size());
+        if (debug_ > 1) {
+          PHI const& p = Branches.top();
+          if (debug_ > 1) {
+            mprintf("DEBUG:\t\tPlaced on stack: %s - %s - %s - %s (%zu)\n",
+                    topIn.AtomMaskName(p.ai_).c_str(),
+                    topIn.AtomMaskName(p.aj_).c_str(),
+                    topIn.AtomMaskName(p.ak_).c_str(),
+                    topIn.AtomMaskName(p.al_).c_str(), Branches.size());
+          }
+        }
+      }
+      // Designate lowest index as next
+      atL = atK;
+      atK = atJ;
+      atJ = atI;
+    }
+    //if (debug_it == 1) break; // DEBUG
+    //debug_it++; // DEBUG
+  }
+  if (debug_ > 0)
+    mprintf("DEBUG: Max stack size (%s - %s - %s - ?)= %u\n",
+            topIn.AtomMaskName(atL0).c_str(),
+            topIn.AtomMaskName(atK0).c_str(),
+            topIn.AtomMaskName(atJ0).c_str(),
+            maxStack);
+  return 0;
+}
+
+/** Set up Zmatrix from Cartesian coordinates and topology.
+  * This algorithm attempts to "trace" the molecule in a manner that
+  * should make internal coordinate assignment more "natural".
+  */
+int Zmatrix::SetFromFrame_Trace(Frame const& frameIn, Topology const& topIn, int molnum)
+{
+  if (molnum < 0) {
+    mprinterr("Internal Error: Zmatrix::SetFromFrame(): Negative molecule index.\n");
+    return 1;
+  }
+  if (topIn.Nmol() < 1) {
+    mprinterr("Internal Error: Zmatrix::SetFromFrame(): No molecules.\n");
+    return 1;
+  }
+  IC_.clear();
+  Molecule const& currentMol = topIn.Mol(molnum);
+  unsigned int maxnatom = currentMol.NumAtoms();
+
+  // Keep track of which atoms are associated with an internal coordinate
+  Barray hasIC( topIn.Natom(), false );
+  unsigned int nHasIC = 0;
+
+  // See if we need to assign seed atoms
+  if (!HasCartSeeds()) {
+    // First seed atom will just be first atom TODO lowest index heavy atom?
+    if (autoSetSeeds_simple(frameIn, topIn, currentMol)) {
+    //if (autoSetSeeds(frameIn, topIn, maxnatom, currentMol.MolUnit().Front())) {
+      mprinterr("Error: Could not automatically determine seed atoms.\n");
+      return 1;
+    }
+
+  } else {
+    // Seed atoms already set
+    if (debug_ > 0)
+      mprintf("DEBUG: Cartesian Seed indices: %s %s %s\n",
+              topIn.AtomMaskName(seedAt0_).c_str(),
+              topIn.AtomMaskName(seedAt1_).c_str(),
+              topIn.AtomMaskName(seedAt2_).c_str());
+  }
+  // Add IC seeds
+  if (seedAt0_ != InternalCoords::NO_ATOM)
+    AddIC( InternalCoords(seedAt0_, InternalCoords::NO_ATOM, InternalCoords::NO_ATOM, InternalCoords::NO_ATOM,
+                              0, 0, 0) );
+  if (seedAt1_ != InternalCoords::NO_ATOM)
+    AddIC( InternalCoords(seedAt1_, seedAt0_, InternalCoords::NO_ATOM, InternalCoords::NO_ATOM,
+                              sqrt(DIST2_NoImage(frameIn.XYZ(seedAt1_), frameIn.XYZ(seedAt0_))),
+                              0, 0) );
+  if (seedAt2_ != InternalCoords::NO_ATOM)
+    AddIC( InternalCoords(seedAt2_, seedAt1_, seedAt0_, InternalCoords::NO_ATOM,
+                              sqrt(DIST2_NoImage(frameIn.XYZ(seedAt2_), frameIn.XYZ(seedAt1_))),
+                              CalcAngle(frameIn.XYZ(seedAt2_), frameIn.XYZ(seedAt1_), frameIn.XYZ(seedAt0_))*Constants::RADDEG,
+                              0) );
+  // If there are less than 4 atoms we are done
+  if (maxnatom < 4) return 0;
+  // Seeds are already done
+  MARK(seedAt0_, hasIC, nHasIC);
+  MARK(seedAt1_, hasIC, nHasIC);
+  MARK(seedAt2_, hasIC, nHasIC);
+
+  // Do the remaining atoms.
+  // L - K - J - ?
+  if (traceMol(seedAt0_, seedAt1_, seedAt2_, frameIn, topIn, maxnatom, nHasIC, hasIC)) return 1;
+  // J - K - L - ?
+  if (traceMol(seedAt2_, seedAt1_, seedAt0_, frameIn, topIn, maxnatom, nHasIC, hasIC)) return 1;
+  if (topIn[seedAt1_].Nbonds() > 2) {
+    unsigned int nUnfollowedBranches = 0;
+    for (Atom::bond_iterator bat = topIn[seedAt1_].bondbegin(); bat != topIn[seedAt1_].bondend(); ++bat)
+      if (!hasIC[*bat]) ++nUnfollowedBranches;
+    if (nUnfollowedBranches > 0) {
+      mprintf("Warning: Second seed atom %s has more than 2 bonds.\n", topIn.AtomMaskName(seedAt1_).c_str());
+      // Potential tetrahedral or more.
+      for (Atom::bond_iterator bat = topIn[seedAt1_].bondbegin(); bat != topIn[seedAt1_].bondend(); ++bat) {
+        // Ignore seed atoms
+        if (*bat != seedAt0_ && *bat != seedAt2_) {
+          // Improper based off of seed
+          //     I
+          //     |
+          // L - K - J
+          addIc(*bat, seedAt2_, seedAt1_, seedAt0_, frameIn.XYZ(*bat), frameIn.XYZ(seedAt2_), frameIn.XYZ(seedAt1_), frameIn.XYZ(seedAt0_));
+          MARK(*bat, hasIC, nHasIC);
+          // Follow improper branch if needed: L - K - I - ?
+          if (traceMol(seedAt0_, seedAt1_, *bat, frameIn, topIn, maxnatom, nHasIC, hasIC)) return 1;
+        }
+      }
+    }
+  }
+
+  if (nHasIC < maxnatom) {
+    mprintf("Warning: Not all atoms have an associated internal coordinate.\n");
+  }
+
+  return 0;
+}
+
+/** Setup Zmatrix from Cartesian coordinates/topology. */
+int Zmatrix::SetFromFrame(Frame const& frameIn, Topology const& topIn) {
+  return SetFromFrame_Trace(frameIn, topIn, 0);
+}
+
+/** Setup Zmatrix from Cartesian coordinates/topology. */
+int Zmatrix::SetFromFrame(Frame const& frameIn, Topology const& topIn, int molnum)
+{
+  return SetFromFrame_Trace(frameIn, topIn, molnum);
+}
+
+/** Given two bonded atoms A and B, where B has a depth of at least 2
+  * (i.e., it is possible to have B be atom J where we can form J-K-L),
+  * set up a complete set of internal coordinates involving A and B in the
+  * direction of atom A. This means all internal coordinates with A and B
+  * as I and J (should be only 1), as J and K, and as K and L.
+  */
+int Zmatrix::SetupICsAroundBond(int atA, int atB, Frame const& frameIn, Topology const& topIn,
+                                std::vector<bool> const& atomPositionKnown,
+                                BuildAtom const& AtomA, BuildAtom const& AtomB)
+{
+  if (debug_ > 0)
+    mprintf("DEBUG: SetupICsAroundBond: atA= %s (%i)  atB= %s (%i)\n",
+            topIn.AtomMaskName(atA).c_str(), atA+1,
+            topIn.AtomMaskName(atB).c_str(), atB+1);
+  IC_.clear();
+
+  Barray hasIC( topIn.Natom(), false );
+  unsigned int nHasIC = 0;
+  // Mark known atoms as already having IC
+  for (std::vector<bool>::const_iterator it = atomPositionKnown.begin();
+                                         it != atomPositionKnown.end(); ++it)
+  {
+    if (*it) MARK( it - atomPositionKnown.begin(), hasIC, nHasIC );
+  }
+
+  // First, make sure atom B as a bond depth of at least 2.
+  // Choose K and L atoms given atA is I and atB is J.
+  Atom const& AJ = topIn[atB];
+  typedef std::pair<int,int> Apair;
+  std::vector<Apair> KLpairs;
+  for (Atom::bond_iterator kat = AJ.bondbegin(); kat != AJ.bondend(); ++kat)
+  {
+    if (*kat != atA) {
+      //mprintf("DEBUG: kat= %s\n", topIn.AtomMaskName(*kat).c_str());
+      Atom const& AK = topIn[*kat];
+      for (Atom::bond_iterator lat = AK.bondbegin(); lat != AK.bondend(); ++lat)
+      {
+        if (*lat != atB && *lat != atA) {
+          //mprintf("DEBUG: lat= %s\n", topIn.AtomMaskName(*lat).c_str());
+          KLpairs.push_back( Apair(*kat, *lat) );
+        }
+      }
+    }
+  }
+  if (debug_ > 0) {
+    for (std::vector<Apair>::const_iterator it = KLpairs.begin();
+                                            it != KLpairs.end(); ++it)
+      mprintf("DEBUG:\t\tKL pair %s - %s\n", topIn.AtomMaskName(it->first).c_str(),
+              topIn.AtomMaskName(it->second).c_str());
+  }
+  if (KLpairs.empty()) {
+    mprinterr("Error: SetFromFrameAroundBond(): Could not find an atom pair bonded to atom %s\n",
+              topIn.AtomMaskName(atB).c_str());
+    return 1;
+  }
+  // TODO be smarter about how K and L are selected?
+  double maxMass = topIn[KLpairs[0].first].Mass() + topIn[KLpairs[0].second].Mass();
+  unsigned int maxIdx = 0;
+  for (unsigned int idx = 1; idx < KLpairs.size(); idx++) {
+    double sumMass = topIn[KLpairs[idx].first].Mass() + topIn[KLpairs[idx].second].Mass();
+    if (sumMass > maxMass) {
+      maxMass = sumMass;
+      maxIdx = idx;
+    }
+  }
+  int atk0 = KLpairs[maxIdx].first;
+  int atl0 = KLpairs[maxIdx].second;
+  int modelDebug = 0;
+  if (debug_ > 0) {
+    mprintf("DEBUG: Chosen KL pair: %s - %s\n",topIn.AtomMaskName(atk0).c_str(),
+              topIn.AtomMaskName(atl0).c_str());
+    modelDebug = debug_ - 1;
+  }
+  // ---- I J: Set dist, theta, phi for atA atB K L internal coord ---
+  if (debug_ > 0)
+    mprintf("DEBUG: IC (i j) %i - %i - %i - %i\n", atA+1, atB+1, atk0+1, atl0+1);
+  double newDist = Atom::GetBondLength( topIn[atA].Element(), topIn[atB].Element() );
+  if (debug_ > 0) mprintf("DEBUG:\t\tnewDist= %g\n", newDist);
+  double newTheta = 0;
+  if (Cpptraj::Structure::Model::AssignTheta(newTheta, atA, atB, atk0, topIn, frameIn, atomPositionKnown, modelDebug)) {
+    mprinterr("Error: theta (i j) assignment failed.\n");
+    return 1;
+  }
+  if (debug_ > 0) mprintf("DEBUG:\t\tnewTheta = %g\n", newTheta*Constants::RADDEG);
+  double newPhi = 0;
+  if (Cpptraj::Structure::Model::AssignPhi(newPhi, atA, atB, atk0, atl0, topIn, frameIn,
+                                           atomPositionKnown, AtomB, modelDebug))
+  {
+    mprinterr("Error: phi (i j) assignment failed.\n");
+    return 1;
+  }
+  if (debug_ > 0) mprintf("DEBUG:\t\tnewPhi = %g\n", newPhi*Constants::RADDEG);
+  IC_.push_back(InternalCoords( atA, atB, atk0, atl0, newDist, newTheta*Constants::RADDEG, newPhi*Constants::RADDEG ));
+  if (debug_ > 0) {
+    mprintf("DEBUG: MODEL I J IC: ");
+    IC_.back().printIC(topIn);
+  }
+  MARK( atA, hasIC, nHasIC );
+  // ----- J K: Set up ICs for X atA atB K ---------------------------
+  Atom const& AJ1 = topIn[atA];
+  int ati = -1;
+  //Atom const& AK1 = topIn[atB];
+  //Atom const& AL1 = topIn[atk0];
+  for (Atom::bond_iterator iat = AJ1.bondbegin(); iat != AJ1.bondend(); ++iat)
+  {
+    if (*iat != atB) {
+      if (ati == -1) ati = *iat;
+      // Use existing dist
+      newDist = sqrt( DIST2_NoImage(frameIn.XYZ(*iat), frameIn.XYZ(atA)) );
+      // Set theta for I atA atB
+      newTheta = 0;
+      if (Cpptraj::Structure::Model::AssignTheta(newTheta, *iat, atA, atB, topIn, frameIn, atomPositionKnown, modelDebug)) {
+        mprinterr("Error: theta (j k) assignment failed.\n");
+        return 1;
+      }
+      if (debug_ > 0)
+        mprintf("DEBUG:\t\tnewTheta = %g\n", newTheta*Constants::RADDEG);
+      // Set phi for I atA atB K
+      newPhi = 0;
+      if (Cpptraj::Structure::Model::AssignPhi(newPhi, *iat, atA, atB, atk0, topIn, frameIn,
+                                               atomPositionKnown, AtomA, modelDebug))
+      {
+        mprinterr("Error: phi (j k) assignment failed.\n");
+        return 1;
+      }
+      if (debug_ > 0)
+        mprintf("DEBUG:\t\tnewPhi = %g\n", newPhi*Constants::RADDEG);
+      IC_.push_back(InternalCoords( *iat, atA, atB, atk0, newDist, newTheta*Constants::RADDEG, newPhi*Constants::RADDEG ));
+      if (debug_ > 0) {
+        mprintf("DEBUG: MODEL J K IC: ");
+        IC_.back().printIC(topIn);
+      }
+      MARK( *iat, hasIC, nHasIC );
+      // ----- K L: Set up ICs for X iat atA atB ---------------------
+      /*Atom const& AJ2 = topIn[*iat];
+      for (Atom::bond_iterator i2at = AJ2.bondbegin(); i2at != AJ2.bondend(); ++i2at)
+      {
+        if (*i2at != atA && *i2at != atB && !hasIC[*i2at]) {
+          // Use existing dist and theta
+          newDist = sqrt( DIST2_NoImage(frameIn.XYZ(*i2at), frameIn.XYZ(*iat)) );
+          newTheta = CalcAngle( frameIn.XYZ(*i2at), frameIn.XYZ(*iat), frameIn.XYZ(atA) );
+          // Set phi for X iat atA atB
+          newPhi = 0;
+          if (Cpptraj::Structure::Model::AssignPhi(newPhi, *i2at, *iat, atA, atB, topIn, frameIn, atomPositionKnown, atomChirality)) {
+            mprinterr("Error: phi (k l) assignment failed.\n");
+            return 1;
+          }
+          mprintf("DEBUG:\t\tnewPhi = %g\n", newPhi*Constants::RADDEG);
+          IC_.push_back(InternalCoords( *i2at, *iat, atA, atB, newDist, newTheta*Constants::RADDEG, newPhi*Constants::RADDEG ));
+          mprintf("DEBUG: MODEL K L IC: ");
+          IC_.back().printIC(topIn);
+          MARK( *i2at, hasIC, nHasIC );
+          // Trace from atA *iat *i2at outwards
+          ToTrace.push_back(atA);
+          ToTrace.push_back(*iat);
+          ToTrace.push_back(*i2at);
+          //if (traceMol(atA, *iat, *i2at, frameIn, topIn, topIn.Natom(), nHasIC, hasIC)) return 1;
+        }
+      } */
+    }
+  }
+  // Handle remaining atoms.
+  if (AJ1.Nbonds() > 1) {
+    if (AJ1.Nbonds() == 2) {
+      if (debug_ > 0) mprintf("DEBUG: 2 bonds to %s.\n", topIn.AtomMaskName(atA).c_str());
+      if (traceMol(atB, atA, ati, frameIn, topIn, topIn.Natom(), nHasIC, hasIC))
+        return 1;
+    } else {
+      // 3 or more bonds
+      std::vector<int> const& priority = AtomA.Priority();
+      int at0 = -1;
+      int at1 = -1;
+      std::vector<int> remainingAtoms;
+      if (debug_ > 0) mprintf("DEBUG: %i bonds to %s\n", AJ1.Nbonds(), topIn.AtomMaskName(atA).c_str());
+      for (std::vector<int>::const_iterator it = priority.begin(); it != priority.end(); ++it) {
+        if (*it != atB) {
+          if (debug_ > 0) mprintf("DEBUG:\t\t%s\n", topIn.AtomMaskName(*it).c_str());
+          if (at0 == -1)
+            at0 = *it;
+          else if (at1 == -1)
+            at1 = *it;
+          else
+            remainingAtoms.push_back( *it );
+        }
+      }
+      // at0 atA at1
+      if (traceMol(at1, atA, at0, frameIn, topIn, topIn.Natom(), nHasIC, hasIC))
+        return 1;
+      // at1 atA, at0
+      if (traceMol(at0, atA, at1, frameIn, topIn, topIn.Natom(), nHasIC, hasIC))
+        return 1;
+      // Remaining atoms.
+      for (std::vector<int>::const_iterator it = remainingAtoms.begin(); it != remainingAtoms.end(); ++it) {
+        if (traceMol(at0, atA, *it, frameIn, topIn, topIn.Natom(), nHasIC, hasIC))
+          return 1;
+      }
+    }
+  }
+
+  return 0;
+}
+
+// -----------------------------------------------------------------------------
+/** \return Position of atom I from given internal coordinate. */
+Vec3 Zmatrix::AtomIposition(InternalCoords const& ic, Frame const& frameOut)
+{
+    double rdist = ic.Dist();
+    double theta = ic.Theta();
+    double phi   = ic.Phi();
+
+    double sinTheta = sin(theta * Constants::DEGRAD);
+    double cosTheta = cos(theta * Constants::DEGRAD);
+    double sinPhi   = sin(phi   * Constants::DEGRAD);
+    double cosPhi   = cos(phi   * Constants::DEGRAD);
+
+    // NOTE: Want -x
+    Vec3 xyz( -(rdist * cosTheta),
+                rdist * cosPhi * sinTheta,
+                rdist * sinPhi * sinTheta );
+
+    Vec3 posL = Vec3( frameOut.XYZ( ic.AtL()) );
+    Vec3 posK = Vec3( frameOut.XYZ( ic.AtK()) );
+    Vec3 posJ = Vec3( frameOut.XYZ( ic.AtJ()) );
+
+    Vec3 LK = posK - posL;
+    Vec3 KJ = posJ - posK;
+    KJ.Normalize();
+    Vec3 Norm = LK.Cross(KJ);
+    Norm.Normalize();
+    Vec3 NxKJ = Norm.Cross(KJ);
+
+    Matrix_3x3 Rot( KJ[0], NxKJ[0], Norm[0],
+                    KJ[1], NxKJ[1], Norm[1],
+                    KJ[2], NxKJ[2], Norm[2] );
+
+    Vec3 posI = (Rot * xyz) + posJ;
+
+  return posI;
+}
+
+/** Set Cartesian coordinates in Frame from internal coordinates.
+  * Assume none of the positions in frameOut can be used initially.
+  */
+int Zmatrix::SetToFrame(Frame& frameOut) const {
+  // Track which atoms have Cartesian coords set
+  Barray hasPosition( frameOut.Natom(), false );
+  return SetToFrame(frameOut, hasPosition);
+}
+
+/** Set Cartesian coordinates in Frame from internal coordinates.
+  * Any atom with hasPosition set to true is considered a "good"
+  * position that other ICs can use.
+  * The procedure used here is from:
+  * Parsons et al., "Practical Conversion from Torsion Space to 
+  * Cartesian Space for In Silico Protein Synthesis",
+  * J Comput Chem 26: 1063–1068, 2005.
+  */
+int Zmatrix::SetToFrame(Frame& frameOut, Barray& hasPosition) const {
+  // If any seed positions are defined, set them now
+  if (seedAt0_ != InternalCoords::NO_ATOM) {
+    frameOut.SetXYZ( seedAt0_, seed0Pos_ );
+    hasPosition[ seedAt0_ ] = true;
+  }
+  if (seedAt1_ != InternalCoords::NO_ATOM) {
+    frameOut.SetXYZ( seedAt1_, seed1Pos_ );
+    hasPosition[ seedAt1_ ] = true;
+  }
+  if (seedAt2_ != InternalCoords::NO_ATOM) {
+    frameOut.SetXYZ( seedAt2_, seed2Pos_ );
+    hasPosition[ seedAt2_ ] = true;
+  }
+  // Track which ICs are used
+  Barray isUsed( IC_.size(), false );
+  unsigned int Nused = 0;
+  if (HasCartSeeds()) {
+    if (icseed0_ != InternalCoords::NO_ATOM) MARK(icseed0_, isUsed, Nused);
+    if (icseed1_ != InternalCoords::NO_ATOM) MARK(icseed1_, isUsed, Nused);
+    if (icseed2_ != InternalCoords::NO_ATOM) MARK(icseed2_, isUsed, Nused);
+  } else {
+    // Set positions of atoms from internal coordinate seeds. TODO check for clashes with seedAtX?
+    if (icseed0_ != InternalCoords::NO_ATOM) {
+      // First seed IC atom
+      frameOut.SetXYZ(IC_[icseed0_].AtI(), Vec3(0.0));
+      hasPosition[IC_[icseed0_].AtI()] = true;
+      MARK(icseed0_, isUsed, Nused);
+      // Set position of the second atom.
+      if (icseed1_ != InternalCoords::NO_ATOM) {
+        if (IC_[icseed1_].AtJ() != IC_[icseed0_].AtI()) {
+          mprinterr("Internal Error: Atom j of seed 1 is not Atom i of seed 0.\n");
+          return 1;
+        }
+        double r1 = IC_[icseed1_].Dist();
+        frameOut.SetXYZ(IC_[icseed1_].AtI(), Vec3(r1, 0, 0));
+        hasPosition[IC_[icseed1_].AtI()] = true;
+        MARK(icseed1_, isUsed, Nused);
+        // Set position of the third atom
+        if (icseed2_ != InternalCoords::NO_ATOM) {
+          if (IC_[icseed2_].AtJ() != IC_[icseed1_].AtI()) {
+            mprinterr("Internal Error: Atom j of seed 2 is not Atom i of seed 1.\n");
+            return 1;
+          }
+          if (IC_[icseed2_].AtK() != IC_[icseed0_].AtI()) {
+            mprinterr("Internal Error: Atom k of seed 2 is not Atom i of seed 0.\n");
+            return 1;
+          }
+          double r2 = IC_[icseed2_].Dist();
+          double theta = IC_[icseed2_].Theta();
+
+          double x = r2 * cos(180.0 - theta) * Constants::DEGRAD;
+          double y = r2 * cos(180.0 - theta) * Constants::DEGRAD;
+
+          frameOut.SetXYZ( IC_[icseed2_].AtI(), Vec3(r1 + x, y, 0) );
+          hasPosition[IC_[icseed2_].AtI()] = true;
+          MARK(icseed2_, isUsed, Nused);
+        } // END seed atom 2
+      } // END seed atom 1
+    } // END seed atom 0
+  } // END Does not have Cart. seeds
+  // Find the lowest unused IC
+  unsigned int lowestUnusedIC = 0;
+  for (; lowestUnusedIC < IC_.size(); ++lowestUnusedIC)
+    if (!isUsed[lowestUnusedIC]) break;
+  if (debug_ > 0) mprintf("DEBUG: Lowest unused IC: %u\n", lowestUnusedIC+1);
+
+  // Loop over remaining ICs 
+  while (Nused < IC_.size()) {
+    // Find the next IC that is not yet used.
+    unsigned int idx = lowestUnusedIC;
+    bool findNextIC = true;
+    while (findNextIC) {
+      while (idx < IC_.size() && isUsed[idx]) idx++;
+      if (idx >= IC_.size()) {
+        mprinterr("Error: Could not find next IC to use.\n");
+        return 1;
+      }
+      // All 3 of the connecting atoms must be set
+      if (hasPosition[ IC_[idx].AtJ() ] &&
+          hasPosition[ IC_[idx].AtK() ] &&
+          hasPosition[ IC_[idx].AtL() ])
+      {
+        findNextIC = false;
+      } else
+        idx++;
+    } // END loop finding next atom to set
+    if (debug_ > 0) mprintf("DEBUG: Next IC to use is %u\n", idx+1);
+
+    InternalCoords const& ic = IC_[idx];
+    Vec3 posI = AtomIposition(ic, frameOut);
+
+    frameOut.SetXYZ( ic.AtI(), posI );
+    hasPosition[ ic.AtI() ] = true;
+    MARK(idx, isUsed, Nused);
+
+    // Next lowest unused IC
+    for (; lowestUnusedIC < IC_.size(); ++lowestUnusedIC)
+      if (!isUsed[lowestUnusedIC]) break;
+
+
+    //break; // DEBUG
+  } // END loop over internal coordinates
+
+  return 0;
+}
diff --git a/src/Structure/Zmatrix.h b/src/Structure/Zmatrix.h
new file mode 100644
index 0000000000..d778e34145
--- /dev/null
+++ b/src/Structure/Zmatrix.h
@@ -0,0 +1,97 @@
+#ifndef INC_STRUCTURE_ZMATRIX_H
+#define INC_STRUCTURE_ZMATRIX_H
+#include "InternalCoords.h"
+#include "StructureEnum.h"
+#include "../Vec3.h"
+class Frame;
+class Topology;
+class Molecule;
+namespace Cpptraj {
+namespace Structure {
+class BuildAtom;
+/// Hold internal coordinates for a system.
+class Zmatrix {
+    typedef std::vector<InternalCoords> ICarray;
+  public:
+    typedef std::vector<bool> Barray;
+    /// CONSTRUCTOR
+    Zmatrix();
+    /// Set debug level
+    void SetDebug(int d) { debug_ = d; }
+    /// Print to stdout
+    void print(Topology*) const;
+    /// Print to stdout, no atom names
+    void print() const { print(0); }
+
+    /// \reserve space for # of internal coords TODO zero out seeds?
+    void reserve(unsigned int n) { IC_.reserve( n ); }
+    /// Clear the Zmatrix
+    void clear();
+    /// Add internal coordinate
+    int AddIC(InternalCoords const&);
+    /// Set specified IC
+    void SetIC(unsigned int, InternalCoords const&);
+
+    /// Set seed atoms from frame/top
+    int SetSeedPositions(Frame const&, Topology const&, int, int, int);
+
+    /// Convert specifed molecule of Frame/Topology to internal coordinates array
+    int SetFromFrame(Frame const&, Topology const&, int);
+    /// Convert molecule 0 of Frame/Topology to internal coordinates array
+    int SetFromFrame(Frame const&, Topology const&);
+    /// Get internal coordinates around bond in one direction.
+    int SetupICsAroundBond(int, int, Frame const&, Topology const&,
+                           std::vector<bool> const&, BuildAtom const&, BuildAtom const&);
+
+    /// Set Frame from internal coords
+    int SetToFrame(Frame&) const;
+    /// Set Frame from internal coords with some positions already set
+    int SetToFrame(Frame&, Barray&) const;
+
+    typedef ICarray::const_iterator const_iterator;
+    const_iterator begin() const { return IC_.begin(); }
+    const_iterator end()   const { return IC_.end(); }
+
+    /// \return Specified internal coord
+    InternalCoords const& operator[](int idx) const { return IC_[idx]; }
+    /// \return Array containing indices of ICs involving specified atom I
+    std::vector<int> AtomI_indices(int) const;
+    /// \return number of internal coords
+    unsigned int N_IC() const { return IC_.size(); }
+    /// \return memory usage in bytes
+    unsigned int sizeInBytes() const { return (7*sizeof(int)) +
+                                              (9*sizeof(double)) + // 3 Vec3
+                                              (IC_.size() * InternalCoords::sizeInBytes()); }
+
+    /// \return XYZ position of atom I for given internal coordinate
+    static Vec3 AtomIposition(InternalCoords const&, Frame const&);
+  private:
+    typedef std::vector<int> Iarray;
+    /// Simple version of auto set seeds based on connectivity only
+    int autoSetSeeds_simple(Frame const&, Topology const&, Molecule const&);
+    /// Calculate and add an internal coordinate given indices and Cartesian coords.
+    void addIc(int,int,int,int,const double*,const double*,const double*,const double*);
+    /// Add internal coordiantes by tracing a molecule
+    int traceMol(int, int, int, Frame const&, Topology const&, unsigned int, unsigned int&, Barray&);
+    /// Convert from Cartesian to minimal Zmatrix by tracing a molecule
+    int SetFromFrame_Trace(Frame const&, Topology const&, int);
+    /// \return True if IC seeds are set
+    //bool HasICSeeds() const;
+    /// \return True if Cartesian seeds are set
+    bool HasCartSeeds() const;
+
+    int debug_;     ///< Print debug info
+    ICarray IC_;    ///< Hold internal coordinates for all atoms
+    int icseed0_;   ///< Index into IC_ of first seed
+    int icseed1_;   ///< Index into IC_ of second seed
+    int icseed2_;   ///< Index into IC_ of third seed
+    Vec3 seed0Pos_; ///< Seed 0 xyz
+    Vec3 seed1Pos_; ///< Seed 1 xyz
+    Vec3 seed2Pos_; ///< Seed 2 xyz
+    int seedAt0_;   ///< Seed 0 topology index if seed0Pos_ is set
+    int seedAt1_;   ///< Seed 1 topology index if seed1Pos_ is set
+    int seedAt2_;   ///< Seed 2 topology index if seed2Pos_ is set
+};
+}
+}
+#endif
diff --git a/src/Structure/structuredepend b/src/Structure/structuredepend
index 2cbff1ef9f..786f57a3d6 100644
--- a/src/Structure/structuredepend
+++ b/src/Structure/structuredepend
@@ -1,9 +1,15 @@
+Builder.o : Builder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h Builder.h Chirality.h InternalCoords.h StructureEnum.h Zmatrix.h
+Chirality.o : Chirality.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Chirality.h StructureEnum.h
 Disulfide.o : Disulfide.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Disulfide.h ResStatArray.h StructureRoutines.h
 FunctionalGroup.o : FunctionalGroup.cpp ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h
 FxnGroupBuilder.o : FxnGroupBuilder.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h FxnGroupBuilder.h StructureRoutines.h Sugar.h SugarToken.h
 HisProt.o : HisProt.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h HisProt.h StructureRoutines.h
+InternalCoords.o : InternalCoords.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h InternalCoords.h
+Model.o : Model.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h Model.h StructureEnum.h
+StructureEnum.o : StructureEnum.cpp StructureEnum.h
 StructureRoutines.o : StructureRoutines.cpp ../Atom.h ../CpptrajStdio.h ../NameType.h ../Residue.h ../SymbolExporting.h StructureRoutines.h
 Sugar.o : Sugar.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Sugar.h SugarToken.h
-SugarBuilder.o : SugarBuilder.cpp ../ArgList.h ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../CharMask.h ../Chirality.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DistRoutines.h ../FileIO.h ../FileName.h ../Frame.h ../ImageOption.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h FunctionalGroup.h FxnGroupBuilder.h LinkAtom.h ResStatArray.h StructureRoutines.h Sugar.h SugarBuilder.h SugarLinkAtoms.h SugarToken.h
+SugarBuilder.o : SugarBuilder.cpp ../ArgList.h ../Atom.h ../AtomMap.h ../AtomMask.h ../AtomType.h ../Box.h ../CharMask.h ../Constants.h ../CoordinateInfo.h ../CpptrajFile.h ../CpptrajStdio.h ../DistRoutines.h ../FileIO.h ../FileName.h ../Frame.h ../ImageOption.h ../MapAtom.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h Chirality.h FunctionalGroup.h FxnGroupBuilder.h LinkAtom.h ResStatArray.h StructureEnum.h StructureRoutines.h Sugar.h SugarBuilder.h SugarLinkAtoms.h SugarToken.h
 SugarLinkAtoms.o : SugarLinkAtoms.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../FileName.h ../Frame.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../StringRoutines.h ../SymbolExporting.h ../Topology.h ../TypeNameHolder.h ../Unit.h ../Vec3.h LinkAtom.h SugarLinkAtoms.h
 SugarToken.o : SugarToken.cpp ../ArgList.h ../CpptrajStdio.h SugarToken.h
+Zmatrix.o : Zmatrix.cpp ../Atom.h ../AtomMask.h ../AtomType.h ../Box.h ../Constants.h ../CoordinateInfo.h ../CpptrajStdio.h ../DistRoutines.h ../FileName.h ../Frame.h ../ImageOption.h ../MaskToken.h ../Matrix_3x3.h ../Molecule.h ../NameType.h ../Parallel.h ../ParameterHolders.h ../ParameterSet.h ../ParameterTypes.h ../Range.h ../ReplicaDimArray.h ../Residue.h ../Segment.h ../SymbolExporting.h ../Topology.h ../TorsionRoutines.h ../TypeNameHolder.h ../Unit.h ../Vec3.h BuildAtom.h InternalCoords.h Model.h StructureEnum.h Zmatrix.h
diff --git a/src/Structure/structurefiles b/src/Structure/structurefiles
index b517cbaf51..0a0a55cc57 100644
--- a/src/Structure/structurefiles
+++ b/src/Structure/structurefiles
@@ -1,11 +1,17 @@
 # Files for Structure subdirectory.
 STRUCTURE_SOURCES= \
+  Builder.cpp \
+  Chirality.cpp \
   Disulfide.cpp \
   FunctionalGroup.cpp \
   FxnGroupBuilder.cpp \
   HisProt.cpp \
+  InternalCoords.cpp \
+  Model.cpp \
+  StructureEnum.cpp \
   StructureRoutines.cpp \
   SugarBuilder.cpp \
   Sugar.cpp \
   SugarLinkAtoms.cpp \
-  SugarToken.cpp
+  SugarToken.cpp \
+  Zmatrix.cpp
diff --git a/src/Topology.cpp b/src/Topology.cpp
index 703e866f3f..fe35eea5c2 100644
--- a/src/Topology.cpp
+++ b/src/Topology.cpp
@@ -38,6 +38,17 @@ const char *Topology::c_str() const {
   return parmName_.c_str();
 }
 
+/** \return count of heavy atoms (ignore hydrogen/extra points). */
+unsigned int Topology::HeavyAtomCount() const {
+  unsigned int hac = 0;
+  for (atom_iterator at = begin(); at != end(); ++at) {
+    if (at->Element() != Atom::HYDROGEN &&
+        at->Element() != Atom::EXTRAPT)
+      hac++;
+  }
+  return hac;
+}
+
 /** Reset all PDB-related info.
   * NOTE: This routine is used by AmbPDB.
   */
@@ -1975,12 +1986,22 @@ void Topology::StripDihedralParmArray(DihedralArray& newDihedralArray, std::vect
 
 // Topology::AddBondArray()
 void Topology::AddBondArray(BondArray const& barray, BondParmArray const& bp, int atomOffset) {
-  if (bp.empty())
+  if (bp.empty()) {
     for (BondArray::const_iterator bond = barray.begin(); bond != barray.end(); ++bond)
       AddBond( bond->A1() + atomOffset, bond->A2() + atomOffset );
-  else
-    for (BondArray::const_iterator bond = barray.begin(); bond != barray.end(); ++bond)
-      AddBond( bond->A1() + atomOffset, bond->A2() + atomOffset, bp[bond->Idx()] );
+  } else {
+    bool missingParameters = false;
+    for (BondArray::const_iterator bond = barray.begin(); bond != barray.end(); ++bond) {
+      if (bond->Idx() > -1)
+        AddBond( bond->A1() + atomOffset, bond->A2() + atomOffset, bp[bond->Idx()] );
+      else {
+        missingParameters = true;
+        AddBond( bond->A1() + atomOffset, bond->A2() + atomOffset );
+      }
+    }
+    if (missingParameters)
+      mprintf("Warning: Some bonds were missing parameters.\n");
+  }
 }
 
 // Topology::AddAngleArray()
diff --git a/src/Topology.h b/src/Topology.h
index 7f0e67ca6e..cc670fad38 100644
--- a/src/Topology.h
+++ b/src/Topology.h
@@ -47,6 +47,8 @@ class Topology {
     const Atom &operator[](int idx)              const { return atoms_[idx];    }
     std::vector<Atom> const& Atoms()             const { return atoms_;         }
     Atom& SetAtom(int idx)                             { return atoms_[idx]; }
+    /// \return Count of "heavy" atoms (non-hydrogen, non-extra point)
+    unsigned int HeavyAtomCount() const;
     // ----- Amber Extra Info --------------------
     std::vector<NameType> const& TreeChainClassification() const { return tree_;   }
     std::vector<int>      const& JoinArray()               const { return ijoin_;  }
diff --git a/src/Version.h b/src/Version.h
index 7c898f252d..f4967b2642 100644
--- a/src/Version.h
+++ b/src/Version.h
@@ -12,7 +12,7 @@
  * Whenever a number that precedes <revision> is incremented, all subsequent
  * numbers should be reset to 0.
  */
-#define CPPTRAJ_INTERNAL_VERSION "V6.20.6"
+#define CPPTRAJ_INTERNAL_VERSION "V6.21.0"
 /// PYTRAJ relies on this
 #define CPPTRAJ_VERSION_STRING CPPTRAJ_INTERNAL_VERSION
 #endif
diff --git a/src/cpptrajdepend b/src/cpptrajdepend
index e2c8c578a7..e379d7ca83 100644
--- a/src/cpptrajdepend
+++ b/src/cpptrajdepend
@@ -29,7 +29,7 @@ Action_Dihedral.o : Action_Dihedral.cpp Action.h ActionState.h Action_Dihedral.h
 Action_DihedralRMS.o : Action_DihedralRMS.cpp Action.h ActionState.h Action_DihedralRMS.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Action_Dipole.o : Action_Dipole.cpp Action.h ActionState.h Action_Dipole.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h Grid.h GridAction.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Action_DistRmsd.o : Action_DistRmsd.cpp Action.h ActionState.h Action_DistRmsd.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceAction.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Action_Distance.o : Action_Distance.cpp Action.h ActionState.h Action_Distance.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Action_Distance.o : Action_Distance.cpp Action.h ActionState.h Action_Distance.h ArgList.h AssociatedData.h AssociatedData_NOE.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Action_Energy.o : Action_Energy.cpp Action.h ActionState.h Action_Energy.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy.h EnergyArray.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h Ewald_Regular.h ExclusionArray.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SplineFxnTable.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h helpme_standalone.h
 Action_Esander.o : Action_Esander.cpp Action.h ActionState.h Action_Esander.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h Energy_Sander.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Action_FilterByData.o : Action_FilterByData.cpp Action.h ActionState.h Action_FilterByData.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
@@ -55,7 +55,7 @@ Action_MultiDihedral.o : Action_MultiDihedral.cpp Action.h ActionState.h Action_
 Action_MultiPucker.o : Action_MultiPucker.cpp Action.h ActionState.h Action_MultiPucker.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Action_MultiVector.o : Action_MultiVector.cpp Action.h ActionState.h Action_MultiVector.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Action_NAstruct.o : Action_NAstruct.cpp Action.h ActionFrameCounter.h ActionState.h Action_NAstruct.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
-Action_NMRrst.o : Action_NMRrst.cpp Action.h ActionState.h Action_NMRrst.h ArgList.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_float.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h ViewRst.h
+Action_NMRrst.o : Action_NMRrst.cpp Action.h ActionState.h Action_NMRrst.h ArgList.h AssociatedData.h AssociatedData_NOE.h Atom.h AtomMap.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h DataSet_float.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h ViewRst.h
 Action_NativeContacts.o : Action_NativeContacts.cpp Action.h ActionState.h Action_NativeContacts.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h DataSet_integer.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Action_OrderParameter.o : Action_OrderParameter.cpp Action.h ActionState.h Action_OrderParameter.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Action_Outtraj.o : Action_Outtraj.cpp Action.h ActionFrameCounter.h ActionState.h Action_Outtraj.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
@@ -129,7 +129,7 @@ Analysis_RunningAvg.o : Analysis_RunningAvg.cpp ActionState.h Analysis.h Analysi
 Analysis_Slope.o : Analysis_Slope.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Slope.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Analysis_Spline.o : Analysis_Spline.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Spline.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Analysis_State.o : Analysis_State.cpp ActionState.h Analysis.h AnalysisState.h Analysis_State.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Analysis_Statistics.o : Analysis_Statistics.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Statistics.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Analysis_Statistics.o : Analysis_Statistics.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Statistics.h ArgList.h Array1D.h AssociatedData.h AssociatedData_NOE.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_float.h DataSet_integer.h DataSet_string.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Analysis_TI.o : Analysis_TI.cpp ActionState.h Analysis.h AnalysisState.h Analysis_TI.h ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mesh.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Analysis_TICA.o : Analysis_TICA.cpp ActionState.h Analysis.h AnalysisState.h Analysis_TICA.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Analysis_Timecorr.o : Analysis_Timecorr.cpp ActionState.h Analysis.h AnalysisState.h Analysis_Timecorr.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h Corr.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Vector.h DataSet_double.h Dimension.h DispatchObject.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
@@ -137,7 +137,8 @@ Analysis_VectorMath.o : Analysis_VectorMath.cpp ActionState.h Analysis.h Analysi
 Analysis_Wavelet.o : Analysis_Wavelet.cpp ActionFrameCounter.h ActionState.h Analysis.h AnalysisState.h Analysis_Wavelet.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ClusterMap.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixFlt.h Dimension.h DispatchObject.h DistRoutines.h FileIO.h FileName.h FileTypes.h Frame.h ImageOption.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h ProgressBar.h ProgressTimer.h PubFFT.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 ArgList.o : ArgList.cpp ArgList.h CpptrajStdio.h StringRoutines.h
 Array1D.o : Array1D.cpp ArgList.h Array1D.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-AssociatedData.o : AssociatedData.cpp ArgList.h AssociatedData.h CpptrajStdio.h
+AssociatedData_Connect.o : AssociatedData_Connect.cpp ArgList.h AssociatedData.h AssociatedData_Connect.h CpptrajStdio.h
+AssociatedData_NOE.o : AssociatedData_NOE.cpp ArgList.h AssociatedData.h AssociatedData_NOE.h CpptrajStdio.h
 Atom.o : Atom.cpp Atom.h CpptrajStdio.h NameType.h SymbolExporting.h
 AtomMap.o : AtomMap.cpp Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 AtomMask.o : AtomMask.cpp Atom.h AtomMask.h CpptrajStdio.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h SymbolExporting.h Unit.h
@@ -151,7 +152,6 @@ ByteRoutines.o : ByteRoutines.cpp
 CIFfile.o : CIFfile.cpp ArgList.h Atom.h BufferedLine.h CIFfile.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h SymbolExporting.h
 CharMask.o : CharMask.cpp Atom.h CharMask.h CpptrajStdio.h MaskToken.h Molecule.h NameType.h Residue.h Segment.h SymbolExporting.h Unit.h
 CharmmParamFile.o : CharmmParamFile.cpp ArgList.h AtomType.h BufferedLine.h CharmmParamFile.h Constants.h CpptrajFile.h CpptrajStdio.h FileIO.h FileName.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h StringRoutines.h TypeNameHolder.h
-Chirality.o : Chirality.cpp Atom.h AtomMask.h AtomType.h Box.h Chirality.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Cluster/Algorithm.o : Cluster/Algorithm.cpp Cluster/Algorithm.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h CpptrajStdio.h
 Cluster/Algorithm_DBscan.o : Cluster/Algorithm_DBscan.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cluster/Algorithm.h Cluster/Algorithm_DBscan.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Cluster/Algorithm_DPeaks.o : Cluster/Algorithm_DPeaks.cpp ArgList.h AssociatedData.h Cluster/Algorithm.h Cluster/Algorithm_DPeaks.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_Mesh.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h ProgressBar.h Range.h Spline.h TextFormat.h
@@ -186,7 +186,7 @@ ClusterMap.o : ClusterMap.cpp AssociatedData.h ClusterMap.h Constants.h CpptrajF
 Cmd.o : Cmd.cpp Cmd.h DispatchObject.h
 CmdInput.o : CmdInput.cpp CmdInput.h StringRoutines.h
 CmdList.o : CmdList.cpp Cmd.h CmdList.h DispatchObject.h
-Command.o : Command.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_Align.h Action_Angle.h Action_AreaPerMol.h Action_AtomMap.h Action_AtomicCorr.h Action_AtomicFluct.h Action_AutoImage.h Action_Average.h Action_AvgBox.h Action_Bounds.h Action_Box.h Action_Center.h Action_Channel.h Action_CheckChirality.h Action_CheckStructure.h Action_Closest.h Action_ClusterDihedral.h Action_Contacts.h Action_CreateCrd.h Action_CreateReservoir.h Action_DNAionTracker.h Action_DSSP.h Action_Density.h Action_Diffusion.h Action_Dihedral.h Action_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_Keep.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiPucker.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SymmetricRmsd.h Action_Temperature.h Action_Time.h Action_ToroidalDiffusion.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_CalcDiffusion.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_EvalPlateau.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_TICA.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h BoxArgs.h BufferedLine.h CharMask.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h ClusterMap.h Cmd.h CmdInput.h CmdList.h Command.h CompactFrameArray.h ComplexArray.h Constants.h Constraints.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_RemLog.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Deprecated.h DiffusionResults.h DihedralSearch.h Dimension.h DispatchObject.h Energy.h Energy_Sander.h EnsembleIn.h EnsembleOutList.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h ExclusionArray.h Exec.h Exec_AddMissingRes.h Exec_Analyze.h Exec_Calc.h Exec_CatCrd.h Exec_Change.h Exec_ClusterMap.h Exec_CombineCoords.h Exec_Commands.h Exec_CompareClusters.h Exec_CompareEnergy.h Exec_CompareTop.h Exec_CrdAction.h Exec_CrdOut.h Exec_CrdTransform.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Emin.h Exec_ExtendedComparison.h Exec_Flatten.h Exec_GenerateAmberRst.h Exec_Graft.h Exec_Help.h Exec_HmassRepartition.h Exec_LoadCrd.h Exec_LoadTraj.h Exec_ParallelAnalysis.h Exec_ParmBox.h Exec_ParmSolvent.h Exec_ParmStrip.h Exec_ParmWrite.h Exec_ParseTiming.h Exec_PermuteDihedrals.h Exec_Precision.h Exec_PrepareForLeap.h Exec_PrintData.h Exec_Random.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_SequenceAlign.h Exec_Set.h Exec_Show.h Exec_SortEnsembleData.h Exec_SplitCoords.h Exec_System.h Exec_Top.h Exec_Traj.h Exec_UpdateParameters.h Exec_ViewRst.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h GIST_PME.h Grid.h GridAction.h GridBin.h HistBin.h Hungarian.h ImageOption.h ImageTypes.h InputTrajCommon.h MapAtom.h MaskArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h OnlineVarT.h OutputTrajCommon.h PDBfile.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h SplineFxnTable.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h molsurf.h
+Command.o : Command.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h ActionTopWriter.h Action_Align.h Action_Angle.h Action_AreaPerMol.h Action_AtomMap.h Action_AtomicCorr.h Action_AtomicFluct.h Action_AutoImage.h Action_Average.h Action_AvgBox.h Action_Bounds.h Action_Box.h Action_Center.h Action_Channel.h Action_CheckChirality.h Action_CheckStructure.h Action_Closest.h Action_ClusterDihedral.h Action_Contacts.h Action_CreateCrd.h Action_CreateReservoir.h Action_DNAionTracker.h Action_DSSP.h Action_Density.h Action_Diffusion.h Action_Dihedral.h Action_DihedralRMS.h Action_Dipole.h Action_DistRmsd.h Action_Distance.h Action_Energy.h Action_Esander.h Action_FilterByData.h Action_FixAtomOrder.h Action_FixImagedBonds.h Action_GIST.h Action_Grid.h Action_GridFreeEnergy.h Action_HydrogenBond.h Action_Image.h Action_InfraredSpectrum.h Action_Jcoupling.h Action_Keep.h Action_LESsplit.h Action_LIE.h Action_LipidOrder.h Action_MakeStructure.h Action_Mask.h Action_Matrix.h Action_MinImage.h Action_Molsurf.h Action_MultiDihedral.h Action_MultiPucker.h Action_MultiVector.h Action_NAstruct.h Action_NMRrst.h Action_NativeContacts.h Action_OrderParameter.h Action_Outtraj.h Action_PairDist.h Action_Pairwise.h Action_Principal.h Action_Projection.h Action_Pucker.h Action_Radgyr.h Action_Radial.h Action_RandomizeIons.h Action_Remap.h Action_ReplicateCell.h Action_Rmsd.h Action_Rotate.h Action_RunningAvg.h Action_STFC_Diffusion.h Action_Scale.h Action_SetVelocity.h Action_Spam.h Action_Strip.h Action_Surf.h Action_SymmetricRmsd.h Action_Temperature.h Action_Time.h Action_ToroidalDiffusion.h Action_Translate.h Action_Unstrip.h Action_Unwrap.h Action_Vector.h Action_VelocityAutoCorr.h Action_Volmap.h Action_Volume.h Action_Watershell.h Action_XtalSymm.h Analysis.h AnalysisList.h AnalysisState.h Analysis_AmdBias.h Analysis_AutoCorr.h Analysis_Average.h Analysis_CalcDiffusion.h Analysis_Clustering.h Analysis_ConstantPHStats.h Analysis_Corr.h Analysis_CrankShaft.h Analysis_CrdFluct.h Analysis_CrossCorr.h Analysis_CurveFit.h Analysis_Divergence.h Analysis_EvalPlateau.h Analysis_FFT.h Analysis_HausdorffDistance.h Analysis_Hist.h Analysis_IRED.h Analysis_Integrate.h Analysis_KDE.h Analysis_Lifetime.h Analysis_LowestCurve.h Analysis_Matrix.h Analysis_MeltCurve.h Analysis_Modes.h Analysis_MultiHist.h Analysis_Multicurve.h Analysis_Overlap.h Analysis_PhiPsi.h Analysis_Regression.h Analysis_RemLog.h Analysis_Rms2d.h Analysis_RmsAvgCorr.h Analysis_Rotdif.h Analysis_RunningAvg.h Analysis_Slope.h Analysis_Spline.h Analysis_State.h Analysis_Statistics.h Analysis_TI.h Analysis_TICA.h Analysis_Timecorr.h Analysis_VectorMath.h Analysis_Wavelet.h ArgList.h Array1D.h ArrayIterator.h AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h AxisType.h BaseIOtype.h Box.h BoxArgs.h BufferedLine.h CharMask.h Cluster/Algorithm.h Cluster/BestReps.h Cluster/CentroidArray.h Cluster/Cframes.h Cluster/Control.h Cluster/DrawGraph.h Cluster/List.h Cluster/Metric.h Cluster/MetricArray.h Cluster/Node.h Cluster/Sieve.h Cluster/Silhouette.h ClusterMap.h Cmd.h CmdInput.h CmdList.h Command.h CompactFrameArray.h ComplexArray.h Constants.h Constraints.h ControlBlock.h ControlBlock_For.h CoordinateInfo.h Corr.h Cph.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_GridFlt.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_RemLog.h DataSet_Vector.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h Deprecated.h DiffusionResults.h DihedralSearch.h Dimension.h DispatchObject.h Energy.h Energy_Sander.h EnsembleIn.h EnsembleOutList.h Ewald.h EwaldOptions.h Ewald_ParticleMesh.h ExclusionArray.h Exec.h Exec_AddMissingRes.h Exec_Analyze.h Exec_Calc.h Exec_CatCrd.h Exec_Change.h Exec_ClusterMap.h Exec_CombineCoords.h Exec_Commands.h Exec_CompareClusters.h Exec_CompareEnergy.h Exec_CompareTop.h Exec_CrdAction.h Exec_CrdOut.h Exec_CrdTransform.h Exec_CreateSet.h Exec_DataFile.h Exec_DataFilter.h Exec_DataSetCmd.h Exec_Emin.h Exec_ExtendedComparison.h Exec_Flatten.h Exec_GenerateAmberRst.h Exec_Graft.h Exec_Help.h Exec_HmassRepartition.h Exec_LoadCrd.h Exec_LoadTraj.h Exec_ParallelAnalysis.h Exec_ParmBox.h Exec_ParmSolvent.h Exec_ParmStrip.h Exec_ParmWrite.h Exec_ParseTiming.h Exec_PermuteDihedrals.h Exec_Precision.h Exec_PrepareForLeap.h Exec_PrintData.h Exec_Random.h Exec_ReadData.h Exec_ReadEnsembleData.h Exec_ReadInput.h Exec_RotateDihedral.h Exec_RunAnalysis.h Exec_ScaleDihedralK.h Exec_Sequence.h Exec_SequenceAlign.h Exec_Set.h Exec_Show.h Exec_SortEnsembleData.h Exec_SplitCoords.h Exec_System.h Exec_Top.h Exec_Traj.h Exec_UpdateParameters.h Exec_ViewRst.h Exec_Zmatrix.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h GIST_PME.h Grid.h GridAction.h GridBin.h HistBin.h Hungarian.h ImageOption.h ImageTypes.h InputTrajCommon.h MapAtom.h MaskArray.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NC_Routines.h NameType.h NetcdfFile.h OnlineVarT.h OutputTrajCommon.h PDBfile.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PubFFT.h Pucker.h Pucker_PuckerMask.h Pucker_PuckerSearch.h Pucker_PuckerToken.h RPNcalc.h Random.h Range.h ReferenceAction.h ReferenceFrame.h RemdReservoirNC.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h SplineFxnTable.h StructureCheck.h SymbolExporting.h SymmetricRmsdCalc.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h cuda_kernels/GistCudaSetup.cuh helpme_standalone.h molsurf.h
 CompactFrameArray.o : CompactFrameArray.cpp Box.h CompactFrameArray.h CoordinateInfo.h CpptrajStdio.h Matrix_3x3.h Parallel.h ReplicaDimArray.h Vec3.h
 ComplexArray.o : ComplexArray.cpp ArrayIterator.h ComplexArray.h
 Constraints.o : Constraints.cpp ArgList.h Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
@@ -199,11 +199,13 @@ CpptrajFile.o : CpptrajFile.cpp CpptrajFile.h CpptrajStdio.h FileIO.h FileIO_Bzi
 CpptrajState.o : CpptrajState.cpp Action.h ActionList.h ActionState.h Action_CreateCrd.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CompactFrameArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleNavigator.h EnsembleOutList.h FileIO.h FileName.h FileTypes.h Frame.h FrameArray.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Random.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 CpptrajStdio.o : CpptrajStdio.cpp Parallel.h
 CurveFit.o : CurveFit.cpp CurveFit.h
-DataFile.o : DataFile.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h Cluster/Cmatrix_NC.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataIO.h DataIO_AmberEne.h DataIO_CCP4.h DataIO_CharmmFastRep.h DataIO_CharmmOutput.h DataIO_CharmmRepLog.h DataIO_CharmmRtfPrm.h DataIO_Cmatrix_Binary.h DataIO_Cmatrix_NC.h DataIO_Cpout.h DataIO_Evecs.h DataIO_Gnuplot.h DataIO_Grace.h DataIO_Mdout.h DataIO_NetCDF.h DataIO_Numpy.h DataIO_OpenDx.h DataIO_Peaks.h DataIO_RemLog.h DataIO_Std.h DataIO_VecTraj.h DataIO_XVG.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h
+DataFile.o : DataFile.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Cluster/Cframes.h Cluster/Cmatrix_NC.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataFile.h DataIO.h DataIO_AmberEne.h DataIO_AmberLib.h DataIO_AmberPrep.h DataIO_CCP4.h DataIO_CharmmFastRep.h DataIO_CharmmOutput.h DataIO_CharmmRepLog.h DataIO_CharmmRtfPrm.h DataIO_Cmatrix_Binary.h DataIO_Cmatrix_NC.h DataIO_Cpout.h DataIO_Evecs.h DataIO_Gnuplot.h DataIO_Grace.h DataIO_Mdout.h DataIO_NetCDF.h DataIO_Numpy.h DataIO_OpenDx.h DataIO_Peaks.h DataIO_RemLog.h DataIO_Std.h DataIO_VecTraj.h DataIO_XVG.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajectoryFile.h TypeNameHolder.h Unit.h Vec3.h
 DataFileList.o : DataFileList.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h PDBfile.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataFilter.o : DataFilter.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_integer.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO.o : DataIO.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataSet.h DataSetList.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_MatrixDbl.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_AmberEne.o : DataIO_AmberEne.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberEne.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_AmberLib.o : DataIO_AmberLib.cpp ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberLib.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+DataIO_AmberPrep.o : DataIO_AmberPrep.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h BondSearch.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_AmberPrep.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_CCP4.o : DataIO_CCP4.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ByteRoutines.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CCP4.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_CharmmFastRep.o : DataIO_CharmmFastRep.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmFastRep.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_RemLog.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_CharmmOutput.o : DataIO_CharmmOutput.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_CharmmOutput.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
@@ -226,7 +228,7 @@ DataIO_VecTraj.o : DataIO_VecTraj.cpp ActionFrameCounter.h ArgList.h ArrayIterat
 DataIO_XVG.o : DataIO_XVG.cpp ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_XVG.h DataSet.h DataSetList.h DataSet_1D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_double.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataIO_Xplor.o : DataIO_Xplor.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataIO.h DataIO_Xplor.h DataSet.h DataSetList.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_GridFlt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataSet.o : DataSet.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
-DataSetList.o : DataSetList.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Cluster/Cframes.h Cluster/Cmatrix_NC.h CompactFrameArray.h ComplexArray.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_FRM.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_GridDbl.h DataSet_GridFlt.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_PairwiseCache_NC.h DataSet_Parameters.h DataSet_RemLog.h DataSet_StringVar.h DataSet_Tensor.h DataSet_Topology.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_disk.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h SymmetricTensor.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Unit.h Vec3.h
+DataSetList.o : DataSetList.cpp ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Cluster/Cframes.h Cluster/Cmatrix_NC.h CompactFrameArray.h ComplexArray.h Constants.h CoordinateInfo.h Cph.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_3D.h DataSet_Coords.h DataSet_Coords_CRD.h DataSet_Coords_FRM.h DataSet_Coords_REF.h DataSet_Coords_TRJ.h DataSet_GridDbl.h DataSet_GridFlt.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_MatrixFlt.h DataSet_Mesh.h DataSet_Modes.h DataSet_PHREMD.h DataSet_PHREMD_Explicit.h DataSet_PHREMD_Implicit.h DataSet_PairwiseCache.h DataSet_PairwiseCache_MEM.h DataSet_PairwiseCache_NC.h DataSet_Parameters.h DataSet_RemLog.h DataSet_StringVar.h DataSet_Tensor.h DataSet_Topology.h DataSet_Vector.h DataSet_Vector_Scalar.h DataSet_Zmatrix.h DataSet_double.h DataSet_float.h DataSet_integer.h DataSet_integer_disk.h DataSet_integer_mem.h DataSet_pH.h DataSet_string.h DataSet_unsignedInt.h Dimension.h FileIO.h FileName.h Frame.h Grid.h GridBin.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h SymmetricTensor.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajFrameIndex.h Trajin.h TypeNameHolder.h Unit.h Vec3.h
 DataSet_1D.o : DataSet_1D.cpp ArrayIterator.h AssociatedData.h ComplexArray.h Constants.h Corr.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h PubFFT.h Range.h TextFormat.h
 DataSet_3D.o : DataSet_3D.cpp AssociatedData.h Box.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_3D.h Dimension.h FileIO.h FileName.h GridBin.h Matrix_3x3.h MetaData.h Parallel.h Range.h TextFormat.h Vec3.h
 DataSet_Coords.o : DataSet_Coords.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
@@ -253,6 +255,7 @@ DataSet_Tensor.o : DataSet_Tensor.cpp AssociatedData.h CpptrajFile.h DataSet.h D
 DataSet_Topology.o : DataSet_Topology.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Topology.h Dimension.h FileIO.h FileName.h FileTypes.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 DataSet_Vector.o : DataSet_Vector.cpp ArrayIterator.h AssociatedData.h ComplexArray.h Constants.h Corr.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_Vector.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h PubFFT.h Range.h SymbolExporting.h TextFormat.h Vec3.h
 DataSet_Vector_Scalar.o : DataSet_Vector_Scalar.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Vector_Scalar.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h Vec3.h
+DataSet_Zmatrix.o : DataSet_Zmatrix.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Zmatrix.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h TextFormat.h Vec3.h
 DataSet_double.o : DataSet_double.cpp AssociatedData.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_double.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 DataSet_float.o : DataSet_float.cpp AssociatedData.h CpptrajFile.h DataSet.h DataSet_1D.h DataSet_float.h Dimension.h FileIO.h FileName.h MetaData.h Parallel.h Range.h TextFormat.h
 DataSet_integer_disk.o : DataSet_integer_disk.cpp AssociatedData.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_1D.h DataSet_integer.h DataSet_integer_disk.h Dimension.h FileIO.h FileName.h File_TempName.h MetaData.h NC_Routines.h Parallel.h Range.h TextFormat.h
@@ -297,12 +300,12 @@ Exec_CrdTransform.o : Exec_CrdTransform.cpp Action.h ActionList.h ActionState.h
 Exec_CreateSet.o : Exec_CreateSet.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_CreateSet.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h RPNcalc.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_DataFile.o : Exec_DataFile.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataFile.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_DataFilter.o : Exec_DataFilter.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataFilter.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataFilter.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ProgressBar.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_DataSetCmd.o : Exec_DataSetCmd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h ArrayIterator.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Vector.h DataSet_string.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataSetCmd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_DataSetCmd.o : Exec_DataSetCmd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h ArrayIterator.h AssociatedData.h AssociatedData_Connect.h AssociatedData_NOE.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h ComplexArray.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Mat3x3.h DataSet_MatrixDbl.h DataSet_Mesh.h DataSet_Vector.h DataSet_string.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_DataSetCmd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Spline.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Emin.o : Exec_Emin.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h Constraints.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnergyArray.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Emin.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MdOpts.h MetaData.h Minimize_SteepestDescent.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h PotentialFunction.h PotentialTerm.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_ExtendedComparison.o : Exec_ExtendedComparison.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ExtendedComparison.h ExtendedSimilarity.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Flatten.o : Exec_Flatten.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_1D.h DataSet_2D.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Flatten.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OnlineVarT.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_GenerateAmberRst.o : Exec_GenerateAmberRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h DistRoutines.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_GenerateAmberRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h ImageOption.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
-Exec_Graft.o : Exec_Graft.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Graft.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Graft.o : Exec_Graft.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Graft.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Help.o : Exec_Help.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Help.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h ParmFile.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_HmassRepartition.o : Exec_HmassRepartition.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_HmassRepartition.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_LoadCrd.o : Exec_LoadCrd.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_LoadCrd.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h Trajin_Single.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
@@ -324,6 +327,7 @@ Exec_ReadInput.o : Exec_ReadInput.cpp Action.h ActionList.h ActionState.h Analys
 Exec_RotateDihedral.o : Exec_RotateDihedral.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DihedralSearch.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RotateDihedral.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TorsionRoutines.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_RunAnalysis.o : Exec_RunAnalysis.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Cmd.h CmdList.h Command.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_RunAnalysis.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_ScaleDihedralK.o : Exec_ScaleDihedralK.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ScaleDihedralK.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
+Exec_Sequence.o : Exec_Sequence.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h AssociatedData_Connect.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Sequence.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/Builder.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_SequenceAlign.o : Exec_SequenceAlign.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_SequenceAlign.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h OutputTrajCommon.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h TrajectoryFile.h Trajin.h TrajinList.h TrajoutList.h Trajout_Single.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Set.o : Exec_Set.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Set.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h StringRoutines.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_Show.o : Exec_Show.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_StringVar.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Show.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
@@ -334,6 +338,7 @@ Exec_Top.o : Exec_Top.cpp Action.h ActionList.h ActionState.h Analysis.h Analysi
 Exec_Traj.o : Exec_Traj.cpp Action.h ActionFrameCounter.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Traj.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_UpdateParameters.o : Exec_UpdateParameters.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Parameters.h DataSet_Topology.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_UpdateParameters.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 Exec_ViewRst.o : Exec_ViewRst.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h BufferedLine.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_ViewRst.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h ViewRst.h
+Exec_Zmatrix.o : Exec_Zmatrix.cpp Action.h ActionList.h ActionState.h Analysis.h AnalysisList.h AnalysisState.h ArgList.h AssociatedData.h Atom.h AtomMask.h AtomType.h BaseIOtype.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajState.h CpptrajStdio.h DataFile.h DataFileList.h DataSet.h DataSetList.h DataSet_Coords.h DataSet_Coords_REF.h DataSet_Zmatrix.h Dimension.h DispatchObject.h EnsembleIn.h EnsembleOutList.h Exec.h Exec_Zmatrix.h FileIO.h FileName.h FileTypes.h Frame.h FramePtrArray.h InputTrajCommon.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReferenceFrame.h ReplicaDimArray.h ReplicaInfo.h Residue.h Segment.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h TextFormat.h Timer.h Topology.h TrajFrameCounter.h Trajin.h TrajinList.h TrajoutList.h TypeNameHolder.h Unit.h Vec3.h
 ExtendedSimilarity.o : ExtendedSimilarity.cpp AssociatedData.h Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h Dimension.h ExtendedSimilarity.h FileIO.h FileName.h Frame.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h TextFormat.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 ExternalFxn.o : ExternalFxn.cpp Random.h
 FileIO_Bzip2.o : FileIO_Bzip2.cpp CpptrajStdio.h FileIO.h FileIO_Bzip2.h
@@ -428,15 +433,21 @@ SpaceGroup.o : SpaceGroup.cpp Matrix_3x3.h Parallel.h SpaceGroup.h Vec3.h
 Spline.o : Spline.cpp CpptrajStdio.h Spline.h
 SplineFxnTable.o : SplineFxnTable.cpp Constants.h CpptrajStdio.h Spline.h SplineFxnTable.h StringRoutines.h
 StringRoutines.o : StringRoutines.cpp CpptrajStdio.h StringRoutines.h
+Structure/Builder.o : Structure/Builder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/Builder.h Structure/Chirality.h Structure/InternalCoords.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Chirality.o : Structure/Chirality.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Chirality.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/Disulfide.o : Structure/Disulfide.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Disulfide.h Structure/ResStatArray.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/FunctionalGroup.o : Structure/FunctionalGroup.cpp Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/FxnGroupBuilder.o : Structure/FxnGroupBuilder.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/HisProt.o : Structure/HisProt.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/HisProt.h Structure/StructureRoutines.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/InternalCoords.o : Structure/InternalCoords.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/InternalCoords.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
+Structure/Model.o : Structure/Model.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/Model.h Structure/StructureEnum.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Structure/StructureEnum.o : Structure/StructureEnum.cpp Structure/StructureEnum.h
 Structure/StructureRoutines.o : Structure/StructureRoutines.cpp Atom.h CpptrajStdio.h NameType.h Residue.h Structure/StructureRoutines.h SymbolExporting.h
 Structure/Sugar.o : Structure/Sugar.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Sugar.h Structure/SugarToken.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
-Structure/SugarBuilder.o : Structure/SugarBuilder.cpp ArgList.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h CharMask.h Chirality.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/LinkAtom.h Structure/ResStatArray.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarLinkAtoms.h Structure/SugarToken.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
+Structure/SugarBuilder.o : Structure/SugarBuilder.cpp ArgList.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DistRoutines.h FileIO.h FileName.h Frame.h ImageOption.h MapAtom.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/Chirality.h Structure/FunctionalGroup.h Structure/FxnGroupBuilder.h Structure/LinkAtom.h Structure/ResStatArray.h Structure/StructureEnum.h Structure/StructureRoutines.h Structure/Sugar.h Structure/SugarBuilder.h Structure/SugarLinkAtoms.h Structure/SugarToken.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 Structure/SugarLinkAtoms.o : Structure/SugarLinkAtoms.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h FileName.h Frame.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StringRoutines.h Structure/LinkAtom.h Structure/SugarLinkAtoms.h SymbolExporting.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 Structure/SugarToken.o : Structure/SugarToken.cpp ArgList.h CpptrajStdio.h Structure/SugarToken.h
+Structure/Zmatrix.o : Structure/Zmatrix.cpp Atom.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h Structure/BuildAtom.h Structure/InternalCoords.h Structure/Model.h Structure/StructureEnum.h Structure/Zmatrix.h SymbolExporting.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 StructureCheck.o : StructureCheck.cpp Atom.h AtomMask.h AtomType.h Box.h CharMask.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h ExclusionArray.h FileName.h Frame.h ImageOption.h MaskToken.h Matrix_3x3.h Molecule.h NameType.h PairList.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StructureCheck.h SymbolExporting.h Timer.h Topology.h TypeNameHolder.h Unit.h Vec3.h
 StructureMapper.o : StructureMapper.cpp AssociatedData.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajFile.h CpptrajStdio.h DataSet.h DataSet_Coords.h DataSet_Coords_REF.h Dimension.h FileIO.h FileName.h Frame.h MapAtom.h MaskToken.h Matrix_3x3.h MetaData.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h StructureMapper.h SymbolExporting.h TextFormat.h Topology.h TorsionRoutines.h TypeNameHolder.h Unit.h Vec3.h
 SymmetricRmsdCalc.o : SymmetricRmsdCalc.cpp ArrayIterator.h Atom.h AtomMap.h AtomMask.h AtomType.h Box.h Constants.h CoordinateInfo.h CpptrajStdio.h DistRoutines.h FileName.h Frame.h Hungarian.h ImageOption.h MapAtom.h MaskToken.h Matrix.h Matrix_3x3.h Molecule.h NameType.h Parallel.h ParameterHolders.h ParameterSet.h ParameterTypes.h Range.h ReplicaDimArray.h Residue.h Segment.h SymbolExporting.h SymmetricRmsdCalc.h Topology.h TypeNameHolder.h Unit.h Vec3.h
diff --git a/src/cpptrajfiles b/src/cpptrajfiles
index 224bdaae47..2d534859fb 100644
--- a/src/cpptrajfiles
+++ b/src/cpptrajfiles
@@ -140,7 +140,8 @@ COMMON_SOURCES= \
         Analysis_Wavelet.cpp \
         ArgList.cpp \
         Array1D.cpp \
-        AssociatedData.cpp \
+        AssociatedData_Connect.cpp \
+        AssociatedData_NOE.cpp \
         Atom.cpp \
         AtomMap.cpp \
         AtomMask.cpp \
@@ -153,7 +154,6 @@ COMMON_SOURCES= \
         ByteRoutines.cpp \
         CharMask.cpp \
         CharmmParamFile.cpp \
-        Chirality.cpp \
         CIFfile.cpp \
         ClusterMap.cpp \
         Cmd.cpp \
@@ -175,6 +175,8 @@ COMMON_SOURCES= \
         DataFilter.cpp \
         DataIO.cpp \
         DataIO_AmberEne.cpp \
+        DataIO_AmberLib.cpp \
+        DataIO_AmberPrep.cpp \
         DataIO_CCP4.cpp \
         DataIO_CharmmFastRep.cpp \
         DataIO_CharmmOutput.cpp \
@@ -231,6 +233,7 @@ COMMON_SOURCES= \
         DataSet_StringVar.cpp \
         DataSet_Tensor.cpp \
         DataSet_unsignedInt.cpp \
+        DataSet_Zmatrix.cpp \
         Deprecated.cpp \
         DihedralSearch.cpp \
         DiffusionResults.cpp \
@@ -295,6 +298,7 @@ COMMON_SOURCES= \
         Exec_RunAnalysis.cpp \
         Exec_ScaleDihedralK.cpp \
         Exec_Set.cpp \
+        Exec_Sequence.cpp \
         Exec_SequenceAlign.cpp \
         Exec_Show.cpp \
         Exec_SortEnsembleData.cpp \
@@ -304,6 +308,7 @@ COMMON_SOURCES= \
         Exec_Traj.cpp \
         Exec_UpdateParameters.cpp \
         Exec_ViewRst.cpp \
+        Exec_Zmatrix.cpp \
         ExtendedSimilarity.cpp \
         File_TempName.cpp \
         FileIO_Bzip2.cpp \
diff --git a/test/Makefile b/test/Makefile
index efc11e1fd6..483b3486a7 100644
--- a/test/Makefile
+++ b/test/Makefile
@@ -524,6 +524,18 @@ test.calcdiffusion:
 test.parsetiming:
 	@-cd Test_ParseTiming && ./RunTest.sh $(OPT)
 
+test.readprep:
+	@-cd Test_ReadPrep && ./RunTest.sh $(OPT)
+
+test.zmatrix:
+	@-cd Test_Zmatrix && ./RunTest.sh $(OPT)
+
+test.readoff:
+	@-cd Test_ReadOFF && ./RunTest.sh $(OPT)
+
+test.sequence:
+	@-cd Test_Sequence && ./RunTest.sh $(OPT)
+
 # Every test target should go here.
 COMPLETETESTS=test.general \
               test.strip \
@@ -689,7 +701,11 @@ COMPLETETESTS=test.general \
               test.avgbox \
               test.tordiff \
               test.calcdiffusion \
-              test.parsetiming
+              test.parsetiming \
+              test.readprep \
+              test.zmatrix \
+              test.readoff \
+              test.sequence
 
 test.all:
 	$(MAKE) test.complete summary
diff --git a/test/Test_Graft/IC.Final.graft.mol2.save b/test/Test_Graft/IC.Final.graft.mol2.save
new file mode 100644
index 0000000000..e4af61be0c
--- /dev/null
+++ b/test/Test_Graft/IC.Final.graft.mol2.save
@@ -0,0 +1,80 @@
+@<TRIPOS>MOLECULE
+Cpptraj Generated mol2 file.
+   34    34     2     0     0
+SMALL
+USER_CHARGES
+
+
+@<TRIPOS>ATOM
+      1 N           5.0262    1.0605    2.4857 N          1 TYR     -0.415700
+      2 H           4.3432    1.6530    2.9356 H          1 TYR      0.271900
+      3 CA          5.5045    1.4387    1.1713 CX         1 TYR     -0.001400
+      4 HA          6.5833    1.5906    1.2064 H1         1 TYR      0.087600
+      5 CB          5.1981    0.3552    0.1428 CT         1 TYR     -0.015200
+      6 HB2         5.6866   -0.5735    0.4378 HC         1 TYR      0.029500
+      7 HB3         5.5697    0.6663   -0.8336 HC         1 TYR      0.029500
+      8 C           4.8470    2.7276    0.6990 C          1 TYR      0.597300
+      9 O           4.0264    3.3055    1.4083 O          1 TYR     -0.567900
+     10 C2          3.6760    0.1340    0.0670 CA         2 PRY      0.033204
+     11 C3          3.1370   -1.1220    0.3590 CA         2 PRY     -0.149016
+     12 H4          3.7940   -1.9290    0.6360 HA         2 PRY      0.153372
+     13 C4          1.7830   -1.3560    0.3010 CA         2 PRY     -0.336291
+     14 H5          1.3750   -2.3240    0.5260 HA         2 PRY      0.167425
+     15 C5          0.9070   -0.3310   -0.0550 CA         2 PRY      0.423974
+     16 O1         -0.4020   -0.6590   -0.0810 OS         2 PRY     -0.391815
+     17 C6          1.4180    0.9200   -0.3470 CA         2 PRY     -0.336291
+     18 H6          0.7760    1.7340   -0.6230 HA         2 PRY      0.167425
+     19 C7          2.7930    1.1360   -0.2830 CA         2 PRY     -0.149016
+     20 H7          3.1680    2.1180   -0.5140 HA         2 PRY      0.153372
+     21 C8         -1.3580    0.3020   -0.4580 CT         2 PRY      0.358047
+     22 C9         -2.6930   -0.3810   -0.4700 CM         2 PRY     -0.496680
+     23 C10        -3.8370    0.0490    0.0400 CM         2 PRY      0.317549
+     24 C11        -5.0960   -0.7730   -0.1000 CT         2 PRY     -0.394216
+     25 C12        -4.0350    1.3480    0.7820 CT         2 PRY     -0.394216
+     26 H8         -1.1210    0.6720   -1.4540 H1         2 PRY      0.001584
+     27 H9         -1.3270    1.1410    0.2250 H1         2 PRY      0.001584
+     28 H10        -2.6800   -1.3290   -0.9820 HA         2 PRY      0.192041
+     29 H11        -5.8660   -0.2140   -0.6260 HC         2 PRY      0.110363
+     30 H12        -5.5010   -1.0240    0.8780 HC         2 PRY      0.110363
+     31 H13        -4.9190   -1.6950   -0.6400 HC         2 PRY      0.110363
+     32 H14        -4.7240    1.9910    0.2380 HC         2 PRY      0.110363
+     33 H15        -3.1210    1.9030    0.9400 HC         2 PRY      0.110363
+     34 H16        -4.4820    1.1590    1.7540 HC         2 PRY      0.110363
+@<TRIPOS>BOND
+    1     1     3 1
+    2     3     5 1
+    3     3     8 1
+    4     8     9 1
+    5    10    11 1
+    6    10    19 1
+    7    11    13 1
+    8    13    15 1
+    9    15    16 1
+   10    15    17 1
+   11    16    21 1
+   12    17    19 1
+   13    21    22 1
+   14    22    23 1
+   15    23    24 1
+   16    23    25 1
+   17     5    10 1
+   18     1     2 1
+   19     3     4 1
+   20     5     6 1
+   21     5     7 1
+   22    11    12 1
+   23    13    14 1
+   24    17    18 1
+   25    19    20 1
+   26    21    26 1
+   27    21    27 1
+   28    22    28 1
+   29    24    29 1
+   30    24    30 1
+   31    24    31 1
+   32    25    32 1
+   33    25    33 1
+   34    25    34 1
+@<TRIPOS>SUBSTRUCTURE
+      1 TYR               1 ****               0 ****  **** 
+      2 PRY              10 ****               0 ****  **** 
diff --git a/test/Test_Graft/IC.Nucleotide.pdb.save b/test/Test_Graft/IC.Nucleotide.pdb.save
new file mode 100644
index 0000000000..59b95bddc8
--- /dev/null
+++ b/test/Test_Graft/IC.Nucleotide.pdb.save
@@ -0,0 +1,33 @@
+ATOM      1  N9   DA     1       4.539  -0.297   3.316  1.00  0.00           N  
+ATOM      2  C8   DA     1       4.337  -0.846   2.077  1.00  0.00           C  
+ATOM      3  H8   DA     1       4.152  -0.207   1.226  1.00  0.00           H  
+ATOM      4  N7   DA     1       4.453  -2.141   2.049  1.00  0.00           N  
+ATOM      5  C5   DA     1       4.754  -2.480   3.363  1.00  0.00           C  
+ATOM      6  C6   DA     1       4.998  -3.708   3.989  1.00  0.00           C  
+ATOM      7  N6   DA     1       4.977  -4.883   3.346  1.00  0.00           N  
+ATOM      8  H61  DA     1       5.161  -5.739   3.851  1.00  0.00           H  
+ATOM      9  H62  DA     1       4.777  -4.914   2.356  1.00  0.00           H  
+ATOM     10  N1   DA     1       5.265  -3.689   5.302  1.00  0.00           N  
+ATOM     11  C2   DA     1       5.285  -2.520   5.935  1.00  0.00           C  
+ATOM     12  H2   DA     1       5.498  -2.482   6.993  1.00  0.00           H  
+ATOM     13  N3   DA     1       5.073  -1.309   5.456  1.00  0.00           N  
+ATOM     14  C4   DA     1       4.806  -1.356   4.133  1.00  0.00           C  
+ATOM     15  C5'  DA     1       1.109   1.452   3.145  1.00  0.00           C  
+ATOM     16  H5'  DA     1       0.981   0.812   4.017  1.00  0.00           H  
+ATOM     17 H5''  DA     1       0.230   2.087   3.028  1.00  0.00           H  
+ATOM     18  C4'  DA     1       2.335   2.328   3.343  1.00  0.00           C  
+ATOM     19  H4'  DA     1       2.082   3.168   3.988  1.00  0.00           H  
+ATOM     20  O4'  DA     1       3.334   1.576   4.098  1.00  0.00           O  
+ATOM     21  C1'  DA     1       4.385   1.163   3.237  1.00  0.00           C  
+ATOM     22  H1'  DA     1       5.314   1.643   3.542  1.00  0.00           H  
+ATOM     23  C3'  DA     1       3.063   2.753   2.066  1.00  0.00           C  
+ATOM     24  H3'  DA     1       2.348   2.823   1.246  1.00  0.00           H  
+ATOM     25  C2'  DA     1       4.053   1.564   1.798  1.00  0.00           C  
+ATOM     26  H2'  DA     1       3.856   1.107   0.829  1.00  0.00           H  
+ATOM     27  O3'  DA     1       3.851   3.932   2.147  1.00  0.00           O  
+ATOM     28  P    DA     1      -0.042  -0.302   1.764  0.00  0.00           P  
+ATOM     29  O1P  DA     1      -1.186   0.613   1.641  0.00  0.00           O  
+ATOM     30  O2P  DA     1       0.290  -1.365   0.804  0.00  0.00           O  
+ATOM     31  O5'  DA     1       1.283   0.644   1.978  0.00  0.00           O  
+TER      32       DA     1 
+END   
diff --git a/test/Test_Graft/Nucleotide.mol2.save b/test/Test_Graft/Nucleotide.charge.mol2.save
similarity index 100%
rename from test/Test_Graft/Nucleotide.mol2.save
rename to test/Test_Graft/Nucleotide.charge.mol2.save
diff --git a/test/Test_Graft/RunTest.sh b/test/Test_Graft/RunTest.sh
index c6952006e2..e5b32c2f2b 100755
--- a/test/Test_Graft/RunTest.sh
+++ b/test/Test_Graft/RunTest.sh
@@ -2,7 +2,8 @@
 
 . ../MasterTest.sh
 
-CleanFiles cpptraj.in Final.graft.mol2 Nucleotide.pdb Nucleotide.mol2
+CleanFiles cpptraj.in Final.graft.mol2 Nucleotide.pdb Nucleotide.charge.mol2 \
+           IC.Final.graft.mol2 IC.Nucleotide.pdb
 TESTNAME='Graft test'
 Requires notparallel
 
@@ -31,12 +32,39 @@ graft \
   tgtmask @C,O,CA,HA,N,H,CB,HB2,HB3 \
   bond :1@CB,:1@C2
 crdout Final Final.graft.mol2
-
+zmatrix Final out zFinal.dat
 EOF
   RunCpptraj "$TESTNAME, Prenylated Tyrosine"
   DoTest Final.graft.mol2.save Final.graft.mol2
 }
 
+# Combine Tyr FF14SB backbone + CB with PRY fragment, use internal coords
+TyrPryIC() {
+  cat > cpptraj.in <<EOF
+set TYRFILE = ../Test_CombineCrd/Tyr.mol2
+# Load the target
+parm \$TYRFILE 
+loadcrd \$TYRFILE parmindex 0 name TYR
+
+# Load the source
+set PRYFILE= ../Test_CombineCrd/PRY-gauss-fragment.mol2
+parm \$PRYFILE
+loadcrd \$PRYFILE parmindex 1 name PRY
+
+graft ic \
+  tgt TYR \
+  src PRY \
+  name Final \
+  srcmask !(@1-4) \
+  tgtmask @C,O,CA,HA,N,H,CB,HB2,HB3 \
+  bond :1@CB,:1@C2
+crdout Final IC.Final.graft.mol2
+zmatrix Final out zicFinal.dat
+EOF
+  RunCpptraj "$TESTNAME, Prenylated Tyrosine (internal coords)"
+  DoTest IC.Final.graft.mol2.save IC.Final.graft.mol2
+}
+
 # Link nucleic acid base + sugar + phosphate
 DNA() {
   cat > cpptraj.in <<EOF
@@ -78,6 +106,45 @@ EOF
   DoTest Nucleotide.pdb.save Nucleotide.pdb
 }
 
+# Link nucleic acid base + sugar + phosphate, IC
+DNAic() {
+  cat > cpptraj.in <<EOF
+for FILE in template-sugar.pdb,template-dimethylphosphate.pdb,template-base-adenine.pdb NAME in Sugar,Phos,Base
+  parm \$FILE
+  loadcrd \$FILE name \$NAME parm \$FILE
+done
+list
+# Base + Sugar
+graft ic \\
+  tgt Base \\
+  src Sugar \\
+  name BaseSugar \\
+  tgtmask !(@C1',1H1',2H1',3H1') \\
+  srcmask !(@C10,1H10,2H10,3H10,HO3',O2',HO2') \\
+  bond @N9,@C1'
+zmatrix BaseSugar out zicBaseSugar.dat
+#crdout BaseSugar BaseSugar.mol2
+#quit
+# BaseSugar + Phosphate
+graft ic \\
+  tgt BaseSugar \\
+  src Phos \\
+  name Nucleotide \\
+  tgtmask !(@O5',HO5') \\
+  srcmask !(@C2,H21,H22,H23,O3',C1,H11,H12,H13) \\
+  bond @C5',@O5'
+#crdout Nucleotide Nucleotide.ic.mol2
+# Format the PDB
+change crdset Nucleotide resname from * to DA
+change crdset Nucleotide oresnums of :1 min 1 max 1
+change crdset Nucleotide oresnums of :2 min 1 max 1
+change crdset Nucleotide oresnums of :3 min 1 max 1
+crdout Nucleotide IC.Nucleotide.pdb
+EOF
+  RunCpptraj "$TESTNAME, Construct Nucleic Acid, IC"
+  DoTest IC.Nucleotide.pdb.save IC.Nucleotide.pdb
+}
+
 # Link nucleic acid base + sugar + phosphate, fix charges.
 DNAcharge() {
   cat > cpptraj.in <<EOF
@@ -111,15 +178,17 @@ graft \
   srcmask !(@C3,H4,H5,H6,O1,C1,H1,H2,H3) \
   bond @C1,@O3
 charge crdset Nucleotide *
-crdout Nucleotide Nucleotide.mol2
+crdout Nucleotide Nucleotide.charge.mol2
 quit
 EOF
   RunCpptraj "$TESTNAME, Construct Nucleic Acid and adjust charge"
-  DoTest Nucleotide.mol2.save Nucleotide.mol2
+  DoTest Nucleotide.charge.mol2.save Nucleotide.charge.mol2
 }
 
 TyrPry
+TyrPryIC
 DNA
+DNAic
 DNAcharge
 
 EndTest
diff --git a/test/Test_ReadOFF/Lib.mol2.save b/test/Test_ReadOFF/Lib.mol2.save
new file mode 100644
index 0000000000..3729da3f97
--- /dev/null
+++ b/test/Test_ReadOFF/Lib.mol2.save
@@ -0,0 +1,34 @@
+@<TRIPOS>MOLECULE
+Cpptraj Generated mol2 file.
+   12    11     1     0     0
+SMALL
+USER_CHARGES
+
+
+@<TRIPOS>ATOM
+      1 N           0.0540   -0.2256    0.0153 N          1 CNALA   -0.570310
+      2 H          -0.4149    0.5139    0.5357 H          1 CNALA    0.364710
+      3 CA          1.5127   -0.0215    0.0706 CX         1 CNALA    0.118030
+      4 HA          1.9976   -0.8599   -0.4376 H1         1 CNALA    0.105630
+      5 CB          1.8871    1.2873   -0.6522 CT         1 CNALA   -0.214290
+      6 HB1         1.5308    1.2705   -1.6848 HC         1 CNALA    0.081710
+      7 HB2         1.4452    2.1491   -0.1463 HC         1 CNALA    0.081710
+      8 HB3         2.9715    1.4185   -0.6703 HC         1 CNALA    0.081710
+      9 C           2.0167   -0.0042    1.5042 C          1 CNALA    0.597740
+     10 O           1.3510    0.3674    2.4498 O          1 CNALA   -0.533510
+     11 OXT         3.2954   -0.2516    1.6078 OH         1 CNALA   -0.566290
+     12 HXT         3.6319   -0.4443    0.7168 HO         1 CNALA    0.453160
+@<TRIPOS>BOND
+    1     1     3 1
+    2     3     5 1
+    3     3     9 1
+    4     9    10 1
+    5     9    11 1
+    6     1     2 1
+    7     3     4 1
+    8     5     6 1
+    9     5     7 1
+   10     5     8 1
+   11    11    12 1
+@<TRIPOS>SUBSTRUCTURE
+      1 CNALA              1 ****               0 ****  **** 
diff --git a/test/Test_ReadOFF/RunTest.sh b/test/Test_ReadOFF/RunTest.sh
new file mode 100755
index 0000000000..db36da31aa
--- /dev/null
+++ b/test/Test_ReadOFF/RunTest.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+
+. ../MasterTest.sh
+
+CleanFiles cpptraj.in Lib.mol2
+
+INPUT='-i cpptraj.in'
+
+cat > cpptraj.in <<EOF
+readdata aminocn15ipq_10.0.lib name Lib
+crdout Lib[CNALA] Lib.mol2
+list
+quit
+EOF
+RunCpptraj "Amber OFF format read test"
+DoTest Lib.mol2.save Lib.mol2
+
+EndTest
diff --git a/test/Test_ReadOFF/aminocn15ipq_10.0.lib b/test/Test_ReadOFF/aminocn15ipq_10.0.lib
new file mode 100644
index 0000000000..194c80dee1
--- /dev/null
+++ b/test/Test_ReadOFF/aminocn15ipq_10.0.lib
@@ -0,0 +1,105 @@
+!!index array str
+ "CNALA"
+!entry.CNALA.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+    "N"     "N"     0   1   131072   1   7  -0.57031
+    "H"     "H"     0   1   131072   2   1   0.36471
+    "CA"    "CX"    0   1   131072   3   6   0.11803
+    "HA"    "H1"    0   1   131072   4   1   0.10563
+    "CB"    "CT"    0   1   131072   5   6  -0.21429
+    "HB1"   "HC"    0   1   131072   6   1   0.08171
+    "HB2"   "HC"    0   1   131072   7   1   0.08171
+    "HB3"   "HC"    0   1   131072   8   1   0.08171
+    "C"     "C"     0   1   131072   9   6   0.59774
+    "O"     "O"     0   1   131072  10   8  -0.53351
+    "OXT"   "OH"    0   1   131072  11   8  -0.56629
+    "HXT"   "HO"    0   1   131072  12   1   0.45316
+!entry.CNALA.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "N" "N" 0 -1 0.0
+ "H" "H" 0 -1 0.0
+ "CA" "CX" 0 -1 0.0
+ "HA" "H1" 0 -1 0.0
+ "CB" "CT" 0 -1 0.0
+ "HB1" "HC" 0 -1 0.0
+ "HB2" "HC" 0 -1 0.0
+ "HB3" "HC" 0 -1 0.0
+ "C" "C" 0 -1 0.0
+ "O" "O" 0 -1 0.0
+ "OXT" "OH" 0 -1 0.0
+ "HXT" "HO" 0 -1 0.0
+!entry.CNALA.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CNALA.unit.childsequence single int
+ 2
+!entry.CNALA.unit.connect array int
+ 1
+ 0
+!entry.CNALA.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 3 4 1
+ 3 5 1
+ 3 9 1
+ 5 6 1
+ 5 7 1
+ 5 8 1
+ 9 10 1
+ 9 11 1
+ 11 12 1
+!entry.CNALA.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+ "R" 1 "A" 6
+ "R" 1 "A" 7
+ "R" 1 "A" 8
+ "R" 1 "A" 9
+ "R" 1 "A" 10
+ "R" 1 "A" 11
+ "R" 1 "A" 12
+!entry.CNALA.unit.name single str
+ "CNALA"
+!entry.CNALA.unit.positions table  dbl x  dbl y  dbl z
+ 0.054000 -0.225600 0.015300
+ -0.414900 0.513900 0.535700
+ 1.512700 -0.021500 0.070600
+ 1.997600 -0.859900 -0.437600
+ 1.887100 1.287300 -0.652200
+ 1.530800 1.270500 -1.684800
+ 1.445200 2.149100 -0.146300
+ 2.971500 1.418500 -0.670300
+ 2.016700 -0.004200 1.504200
+ 1.351000 0.367400 2.449800
+ 3.295400 -0.251600 1.607800
+ 3.631900 -0.444300 0.716800
+!entry.CNALA.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 1 0 0 0 0 0
+!entry.CNALA.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "CNALA" 1 13 1 "p" 0
+!entry.CNALA.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.CNALA.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CNALA.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
diff --git a/test/Test_ReadPrep/RunTest.sh b/test/Test_ReadPrep/RunTest.sh
new file mode 100755
index 0000000000..7fda6c2511
--- /dev/null
+++ b/test/Test_ReadPrep/RunTest.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+
+. ../MasterTest.sh
+
+CleanFiles cpptraj.in test1.mol2
+
+INPUT='-i cpptraj.in'
+
+TESTNAME='Test Prep File Read and Zmatrix Functionality'
+
+cat > cpptraj.in <<EOF
+readdata epACE.prepin name ACE
+crdout ACE[*] test1.mol2
+EOF
+RunCpptraj "$TESTNAME"
+DoTest test1.mol2.save test1.mol2
+
+EndTest
diff --git a/test/Test_ReadPrep/epACE.prepin b/test/Test_ReadPrep/epACE.prepin
new file mode 100644
index 0000000000..6cad968c0c
--- /dev/null
+++ b/test/Test_ReadPrep/epACE.prepin
@@ -0,0 +1,26 @@
+    0    0    2
+
+This is a remark line
+molecule.res
+ACE   INT  0
+CORRECT     OMIT DU   BEG
+  0.0000
+   1  DUMM  DU    M    0  -1  -2     0.000      .0        .0      .00000
+   2  DUMM  DU    M    1   0  -1     1.449      .0        .0      .00000
+   3  DUMM  DU    M    2   1   0     1.523   111.21       .0      .00000
+   4  C     C     M    3   2   1     1.540   111.208  -180.000  0.622165
+   5  CH3   CT    3    4   3   2     1.510    13.677  -163.900 -0.184601
+   6  HH31  HC    E    5   4   3     1.088   109.303    15.018  0.065183
+   7  HH32  HC    E    5   4   3     1.088   109.699   136.062  0.065183
+   8  HH33  HC    E    5   4   3     1.090   108.797  -104.299  0.065183
+   9  O     OD    B    4   3   2     1.223   121.156   106.479 -0.633114
+  10  EP1   EP    E    9   4   3    -1.727     0.000     0.000  0.000000
+
+
+LOOP
+
+IMPROPER
+  CH3   +M    C    O
+
+DONE
+STOP
diff --git a/test/Test_ReadPrep/test1.mol2.save b/test/Test_ReadPrep/test1.mol2.save
new file mode 100644
index 0000000000..91cf27ef1a
--- /dev/null
+++ b/test/Test_ReadPrep/test1.mol2.save
@@ -0,0 +1,24 @@
+@<TRIPOS>MOLECULE
+Cpptraj Generated mol2 file.
+    7     6     1     0     0
+SMALL
+USER_CHARGES
+
+
+@<TRIPOS>ATOM
+      1 C           2.8833   -0.5961   -0.0000 C          1 ACE      0.622165
+      2 CH3         1.6792    0.3097    0.0990 CT         1 ACE     -0.184601
+      3 HH31        0.7746   -0.2946    0.1110 HC         1 ACE      0.065183
+      4 HH32        1.7446    0.9090    1.0047 HC         1 ACE      0.065183
+      5 HH33        1.6621    0.9675   -0.7700 HC         1 ACE      0.065183
+      6 O           3.5821   -0.5797   -1.0036 OD         1 ACE     -0.633114
+      7 EP1         4.5687   -0.5565   -2.4208 EP         1 ACE      0.000000
+@<TRIPOS>BOND
+    1     2     1 1
+    2     6     1 1
+    3     7     6 1
+    4     2     3 1
+    5     2     4 1
+    6     2     5 1
+@<TRIPOS>SUBSTRUCTURE
+      1 ACE               1 ****               0 ****  **** 
diff --git a/test/Test_Sequence/Mol.mol2.save b/test/Test_Sequence/Mol.mol2.save
new file mode 100644
index 0000000000..d15e8643b6
--- /dev/null
+++ b/test/Test_Sequence/Mol.mol2.save
@@ -0,0 +1,45 @@
+@<TRIPOS>MOLECULE
+Cpptraj Generated mol2 file.
+   17    16     2     0     0
+SMALL
+USER_CHARGES
+
+
+@<TRIPOS>ATOM
+      1 C1         -1.8623   -1.2984   -0.5952 CT         1 MOC      1.387300
+      2 H2         -2.2353   -2.1775   -1.1026 H1         1 MOC     -0.288000
+      3 H3         -2.2811   -0.4130   -1.0709 H1         1 MOC     -0.288000
+      4 H4         -2.1956   -1.3220    0.4412 H1         1 MOC     -0.288000
+      5 O5         -0.4741   -1.3169   -0.6848 OS         1 MOC     -0.523200
+      6 N           0.0540   -0.2256    0.0153 N          2 CNALA   -0.570310
+      7 H          -0.4149    0.5139    0.5357 H          2 CNALA    0.364710
+      8 CA          1.5127   -0.0215    0.0706 CX         2 CNALA    0.118030
+      9 HA          1.9976   -0.8599   -0.4376 H1         2 CNALA    0.105630
+     10 CB          1.8871    1.2873   -0.6522 CT         2 CNALA   -0.214290
+     11 HB1         1.5308    1.2705   -1.6848 HC         2 CNALA    0.081710
+     12 HB2         1.4452    2.1491   -0.1463 HC         2 CNALA    0.081710
+     13 HB3         2.9715    1.4185   -0.6703 HC         2 CNALA    0.081710
+     14 C           2.0167   -0.0042    1.5042 C          2 CNALA    0.597740
+     15 O           1.3510    0.3674    2.4498 O          2 CNALA   -0.533510
+     16 OXT         3.2954   -0.2516    1.6078 OH         2 CNALA   -0.566290
+     17 HXT         3.6319   -0.4443    0.7168 HO         2 CNALA    0.453160
+@<TRIPOS>BOND
+    1     1     5 1
+    2     6     8 1
+    3     8    10 1
+    4     8    14 1
+    5    14    15 1
+    6    14    16 1
+    7     5     6 1
+    8     1     2 1
+    9     1     3 1
+   10     1     4 1
+   11     6     7 1
+   12     8     9 1
+   13    10    11 1
+   14    10    12 1
+   15    10    13 1
+   16    16    17 1
+@<TRIPOS>SUBSTRUCTURE
+      1 MOC               1 ****               0 ****  **** 
+      2 CNALA              6 ****               0 ****  **** 
diff --git a/test/Test_Sequence/RunTest.sh b/test/Test_Sequence/RunTest.sh
new file mode 100755
index 0000000000..223c04748f
--- /dev/null
+++ b/test/Test_Sequence/RunTest.sh
@@ -0,0 +1,49 @@
+#!/bin/bash
+
+. ../MasterTest.sh
+
+TESTNAME='Sequence tests'
+
+CleanFiles cpptraj.in Mol.mol2 Mol2.mol2 MOC.mol2 CNALA.mol2 \
+           Mol3.mol2 Mol4.mol2
+
+INPUT='-i cpptraj.in'
+
+cat > cpptraj.in <<EOF
+readdata ../Test_ReadOFF/aminocn15ipq_10.0.lib name A15
+readdata cph_nucleic_caps.lib name CAPS
+list
+sequence CAPS[MOC] A15[CNALA] name Mol
+crdout Mol Mol.mol2
+
+sequence libset A15 libset CAPS MOC CNALA name Mol2
+crdout Mol2 Mol2.mol2
+
+crdout CAPS[MOC] MOC.mol2
+crdout A15[CNALA] CNALA.mol2
+EOF
+RunCpptraj "$TESTNAME, library files"
+DoTest Mol.mol2.save Mol.mol2
+DoTest Mol.mol2.save Mol2.mol2
+
+# NOTE: Depends on mol2 generation of previous test
+cat > cpptraj.in <<EOF
+parm MOC.mol2
+loadcrd MOC.mol2 parm MOC.mol2 name MOC
+dataset connect MOC tail 5
+parm CNALA.mol2
+loadcrd CNALA.mol2 parm CNALA.mol2 name CNALA
+dataset connect CNALA head 1
+sequence MOC CNALA name Mol3
+crdout Mol3 Mol3.mol2
+
+dataset connect MOC tailmask @O5
+dataset connect CNALA headmask @N
+sequence MOC CNALA name Mol4
+crdout Mol4 Mol4.mol2
+EOF
+RunCpptraj "$TESTNAME, mol2 files"
+DoTest Mol.mol2.save Mol3.mol2
+DoTest Mol.mol2.save Mol4.mol2
+
+EndTest
diff --git a/test/Test_Sequence/cph_nucleic_caps.lib b/test/Test_Sequence/cph_nucleic_caps.lib
new file mode 100644
index 0000000000..c5bc25e179
--- /dev/null
+++ b/test/Test_Sequence/cph_nucleic_caps.lib
@@ -0,0 +1,119 @@
+!!index array str
+ "CH3"
+ "MOC"
+!entry.CH3.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "C1" "CT" 0 1 131072 1 6 -0.730700
+ "H2" "H1" 0 1 131072 2 1 0.243600
+ "H3" "H1" 0 1 131072 3 1 0.243600
+ "H4" "H1" 0 1 131072 4 1 0.243600
+!entry.CH3.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "C1" "CT" 0 -1 0.0
+ "H2" "H1" 0 -1 0.0
+ "H3" "H1" 0 -1 0.0
+ "H4" "H1" 0 -1 0.0
+!entry.CH3.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CH3.unit.childsequence single int
+ 2
+!entry.CH3.unit.connect array int
+ 1
+ 0
+!entry.CH3.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 1 4 1
+!entry.CH3.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+!entry.CH3.unit.name single str
+ "CH3"
+!entry.CH3.unit.positions table  dbl x  dbl y  dbl z
+ 1.165500 0.188900 1.000000E-04
+ 2.002800 -0.495400 1.000000E-04
+ 1.228600 0.822700 0.883200
+ 1.228700 0.822700 -0.883100
+!entry.CH3.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 0 0 0 0 0 0
+!entry.CH3.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "CH3" 1 5 1 "?" 0
+!entry.CH3.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.CH3.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.CH3.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+!entry.MOC.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt  dbl chg
+ "C1" "CT" 0 1 131072 1 6 1.387300
+ "H2" "H1" 0 1 131072 2 1 -0.288000
+ "H3" "H1" 0 1 131072 3 1 -0.288000
+ "H4" "H1" 0 1 131072 4 1 -0.288000
+ "O5" "OS" 0 1 131072 5 8 -0.523200
+!entry.MOC.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
+ "C1" "CT" 0 -1 0.0
+ "H2" "H1" 0 -1 0.0
+ "H3" "H1" 0 -1 0.0
+ "H4" "H1" 0 -1 0.0
+ "O5" "OS" 0 -1 0.0
+!entry.MOC.unit.boundbox array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.MOC.unit.childsequence single int
+ 2
+!entry.MOC.unit.connect array int
+ 0
+ 5
+!entry.MOC.unit.connectivity table  int atom1x  int atom2x  int flags
+ 1 2 1
+ 1 3 1
+ 1 4 1
+ 1 5 1
+!entry.MOC.unit.hierarchy table  str abovetype  int abovex  str belowtype  int belowx
+ "U" 0 "R" 1
+ "R" 1 "A" 1
+ "R" 1 "A" 2
+ "R" 1 "A" 3
+ "R" 1 "A" 4
+ "R" 1 "A" 5
+!entry.MOC.unit.name single str
+ "MOC"
+!entry.MOC.unit.positions table  dbl x  dbl y  dbl z
+ -1.165500 0.188900 -1.000000E-04
+ -2.002800 -0.495400 -1.000000E-04
+ -1.228600 0.822700 -0.883200
+ -1.228700 0.822700 0.883100
+ 0.0 -0.570800 0.0
+!entry.MOC.unit.residueconnect table  int c1x  int c2x  int c3x  int c4x  int c5x  int c6x
+ 0 0 0 0 0 0
+!entry.MOC.unit.residues table  str name  int seq  int childseq  int startatomx  str restype  int imagingx
+ "MOC" 1 6 1 "?" 0
+!entry.MOC.unit.residuesPdbSequenceNumber array int
+ 0
+!entry.MOC.unit.solventcap array dbl
+ -1.000000
+ 0.0
+ 0.0
+ 0.0
+ 0.0
+!entry.MOC.unit.velocities table  dbl x  dbl y  dbl z
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
+ 0.0 0.0 0.0
diff --git a/test/Test_Zmatrix/0SB.mol2 b/test/Test_Zmatrix/0SB.mol2
new file mode 100644
index 0000000000..1ae0e92d75
--- /dev/null
+++ b/test/Test_Zmatrix/0SB.mol2
@@ -0,0 +1,85 @@
+@<TRIPOS>MOLECULE
+Cpptraj Generated mol2 file.
+   37    37     1     0     0
+SMALL
+USER_CHARGES
+
+
+@<TRIPOS>ATOM
+      1 C2         14.9015   -9.2110  -16.1237 Cy         1 0SB      0.090000
+      2 O6         15.9650   -8.9416  -17.0642 Oy         1 0SB     -0.344000
+      3 C6         15.6470   -8.6291  -18.4365 Cg         1 0SB     -0.008000
+      4 H6         14.9924   -7.7551  -18.4276 H1         1 0SB      0.000000
+      5 C7         16.9306   -8.1911  -19.1806 Cg         1 0SB      0.278000
+      6 H7         16.6223   -7.7157  -20.1129 H1         1 0SB      0.000000
+      7 O7         17.7162   -9.3572  -19.5311 Oh         1 0SB     -0.656000
+      8 H7O        17.2546   -9.8678  -20.2202 Ho         1 0SB      0.390000
+      9 C8         17.8143   -7.1775  -18.3978 Cg         1 0SB      0.367000
+     10 H8         18.2503   -7.6690  -17.5268 H1         1 0SB      0.000000
+     11 O8         16.9766   -6.0764  -17.9315 Oh         1 0SB     -0.704000
+     12 H8O        16.3695   -6.4413  -17.2732 Ho         1 0SB      0.392000
+     13 C9         18.9488   -6.5888  -19.2694 Cg         1 0SB      0.201000
+     14 H9S        19.5899   -7.3870  -19.6435 H1         1 0SB      0.000000
+     15 H9R        18.5275   -6.0629  -20.1275 H1         1 0SB      0.000000
+     16 O9         19.7601   -5.6665  -18.5085 Oh         1 0SB     -0.672000
+     17 H9O        19.1542   -5.1123  -18.0014 Ho         1 0SB      0.393000
+     18 C5         14.8432   -9.7909  -19.0521 Cg         1 0SB      0.523000
+     19 H5         15.4829  -10.6733  -19.1194 H1         1 0SB      0.000000
+     20 N5         14.3746   -9.4120  -20.3984 Ng         1 0SB     -0.669000
+     21 H5N        13.5695   -8.8129  -20.4509 H          1 0SB      0.261000
+     22 C5N        15.0065   -9.7626  -21.5173 C          1 0SB      0.678000
+     23 O5N        16.0693  -10.3734  -21.4932 O          1 0SB     -0.634000
+     24 CME        14.3328   -9.3639  -22.8447 Cg         1 0SB     -0.005000
+     25 H3M        13.6591   -8.5159  -22.7050 Hc         1 0SB      0.000000
+     26 H2M        13.7643  -10.2118  -23.2293 Hc         1 0SB      0.000000
+     27 H1M        15.0945   -9.0868  -23.5750 Hc         1 0SB      0.000000
+     28 C4         13.6278  -10.1430  -18.1484 Cg         1 0SB      0.203000
+     29 H4         12.9278   -9.3048  -18.1549 H1         1 0SB      0.000000
+     30 O4         12.9124  -11.3226  -18.6262 Oh         1 0SB     -0.714000
+     31 H4O        12.5836  -11.1763  -19.5173 Ho         1 0SB      0.390000
+     32 C3         14.0796  -10.3912  -16.6993 Cg         1 0SB      0.133000
+     33 H3E        13.2074  -10.5810  -16.0686 Hc         1 0SB      0.000000
+     34 H3A        14.6688  -11.3112  -16.6672 Hc         1 0SB      0.000000
+     35 C1         15.4479   -9.7079  -14.6785 C          1 0SB      0.979000
+     36 O1B        15.0415   -9.0353  -13.6948 O2         1 0SB     -0.839000
+     37 O1A        16.1893  -10.7171  -14.6127 O2         1 0SB     -0.839000
+@<TRIPOS>BOND
+    1     2     1 1
+    2     3     2 1
+    3     5     3 1
+    4     7     5 1
+    5     9     5 1
+    6    11     9 1
+    7    13     9 1
+    8    16    13 1
+    9    18     3 1
+   10    20    18 1
+   11    22    20 1
+   12    23    22 1
+   13    24    22 1
+   14    28    18 1
+   15    30    28 1
+   16    32    28 1
+   17    35     1 1
+   18    36    35 1
+   19    37    35 1
+   20    32     1 1
+   21     3     4 1
+   22     5     6 1
+   23     7     8 1
+   24     9    10 1
+   25    11    12 1
+   26    13    14 1
+   27    13    15 1
+   28    16    17 1
+   29    18    19 1
+   30    20    21 1
+   31    24    25 1
+   32    24    26 1
+   33    24    27 1
+   34    28    29 1
+   35    30    31 1
+   36    32    33 1
+   37    32    34 1
+@<TRIPOS>SUBSTRUCTURE
+      1 0SB               1 ****               0 ****  **** 
diff --git a/test/Test_Zmatrix/MEX.mol2 b/test/Test_Zmatrix/MEX.mol2
new file mode 100644
index 0000000000..0af6b6b340
--- /dev/null
+++ b/test/Test_Zmatrix/MEX.mol2
@@ -0,0 +1,18 @@
+@<TRIPOS>MOLECULE
+Cpptraj Generated mol2 file.
+    4     3     1     0     0
+SMALL
+USER_CHARGES
+
+
+@<TRIPOS>ATOM
+      1 CH3         7.4849   -0.7179   -1.6206 Cg         1 MEX      0.000000
+      2 H1          6.7230   -0.0077   -1.9247 H1         1 MEX      0.233000
+      3 H2          7.0157   -1.6856   -1.4777 H1         1 MEX      0.000000
+      4 H3          8.2022   -0.8197   -2.4283 H1         1 MEX      0.000000
+@<TRIPOS>BOND
+    1     1     2 1
+    2     1     3 1
+    3     1     4 1
+@<TRIPOS>SUBSTRUCTURE
+      1 MEX               1 ****               0 ****  **** 
diff --git a/test/Test_Zmatrix/RunTest.sh b/test/Test_Zmatrix/RunTest.sh
new file mode 100755
index 0000000000..4c88a0ff5b
--- /dev/null
+++ b/test/Test_Zmatrix/RunTest.sh
@@ -0,0 +1,51 @@
+#!/bin/bash
+
+. ../MasterTest.sh
+
+CleanFiles cpptraj.in zmatrix.dat zmatrix.0SB.dat fromZmatrix.0SB.mol2 \
+           zmatrix.MEX.dat fromZmatrix.MEX.mol2
+
+INPUT='-i cpptraj.in'
+
+TESTNAME='Zmatrix tests'
+
+Basic() {
+  cat > cpptraj.in <<EOF
+parm ../Test_ReadPrep/test1.mol2.save
+loadcrd ../Test_ReadPrep/test1.mol2.save name MyCrd
+zmatrix MyCrd out zmatrix.dat
+EOF
+  RunCpptraj "$TESTNAME, Basic"
+  DoTest zmatrix.dat.save zmatrix.dat
+}
+
+Sugar() {
+  cat > cpptraj.in <<EOF
+parm 0SB.mol2
+loadcrd 0SB.mol2 name 0SB
+zmatrix 0SB out zmatrix.0SB.dat name MyZ
+zmatrix 0SB zset MyZ name MyCrd
+crdout MyCrd fromZmatrix.0SB.mol2
+EOF
+  RunCpptraj "$TESTNAME, Sugar"
+  DoTest zmatrix.0SB.dat.save zmatrix.0SB.dat
+  DoTest 0SB.mol2 fromZmatrix.0SB.mol2
+}
+
+MEX() {
+  cat > cpptraj.in <<EOF
+parm MEX.mol2
+loadcrd MEX.mol2 name MEX
+zmatrix MEX out zmatrix.MEX.dat name MyZ
+zmatrix MEX zset MyZ name MyCrd
+crdout MyCrd fromZmatrix.MEX.mol2
+EOF
+  RunCpptraj "$TESTNAME, methyl"
+  DoTest MEX.mol2 fromZmatrix.MEX.mol2
+}
+
+Basic
+Sugar
+MEX
+
+EndTest
diff --git a/test/Test_Zmatrix/zmatrix.0SB.dat.save b/test/Test_Zmatrix/zmatrix.0SB.dat.save
new file mode 100644
index 0000000000..91dc2649ae
--- /dev/null
+++ b/test/Test_Zmatrix/zmatrix.0SB.dat.save
@@ -0,0 +1,38 @@
+#IC                                                                 MyZ
+       1    1.000    0.000    0.000    0.000    0.000    0.000    0.000
+       2    2.000    1.000    0.000    0.000    1.445    0.000    0.000
+       3    3.000    2.000    1.000    0.000    1.443  119.813    0.000
+       4    4.000    3.000    2.000    1.000    1.092  107.320   57.481
+       5    5.000    3.000    2.000    1.000    1.547  109.628  172.109
+       6    6.000    5.000    3.000    2.000    1.091  107.454 -165.180
+       7    7.000    5.000    3.000    2.000    1.449  109.776   78.456
+       8    8.000    7.000    5.000    3.000    0.974  109.637   69.177
+       9    9.000    5.000    3.000    2.000    1.556  114.437  -45.455
+      10   10.000    9.000    5.000    3.000    1.091  109.581   68.196
+      11   11.000    9.000    5.000    3.000    1.460  109.032  -50.185
+      12   12.000   11.000    9.000    5.000    0.967  107.041   66.841
+      13   13.000    9.000    5.000    3.000    1.547  112.392 -170.254
+      14   14.000   13.000    9.000    5.000    1.090  110.244  -58.947
+      15   15.000   13.000    9.000    5.000    1.091  110.082   60.184
+      16   16.000   13.000    9.000    5.000    1.445  110.975 -179.231
+      17   17.000   16.000   13.000    9.000    0.965  106.902  -44.062
+      18   18.000    3.000    2.000    1.000    1.541  109.366  -58.369
+      19   19.000   18.000    3.000    2.000    1.092  109.164  -66.569
+      20   20.000   18.000    3.000    2.000    1.475  109.673  173.191
+      21   21.000   20.000   18.000    3.000    1.005  117.087  -78.719
+      22   22.000   20.000   18.000    3.000    1.332  123.257   97.438
+      23   23.000   22.000   20.000   18.000    1.226  121.726   -3.821
+      24   24.000   22.000   20.000   18.000    1.541  116.620  176.070
+      25   25.000   24.000   22.000   20.000    1.092  111.126   23.276
+      26   26.000   24.000   22.000   20.000    1.091  109.294  -97.180
+      27   27.000   24.000   22.000   20.000    1.091  109.699  143.390
+      28   28.000   18.000    3.000    2.000    1.555  110.258   52.047
+      29   29.000   28.000   18.000    3.000    1.092  108.890   66.493
+      30   30.000   28.000   18.000    3.000    1.460  112.071 -174.457
+      31   31.000   30.000   28.000   18.000    0.961  110.371  -59.820
+      32   32.000   28.000   18.000    3.000    1.538  110.763  -52.775
+      33   33.000   32.000   28.000   18.000    1.093  109.712  176.806
+      34   34.000   32.000   28.000   18.000    1.093  108.775  -68.268
+      35   35.000    1.000    2.000    3.000    1.623  112.883  173.396
+      36   36.000   35.000    1.000    2.000    1.259  115.055  125.259
+      37   37.000   35.000    1.000    2.000    1.254  119.483  -56.528
diff --git a/test/Test_Zmatrix/zmatrix.dat.save b/test/Test_Zmatrix/zmatrix.dat.save
new file mode 100644
index 0000000000..a01118dc98
--- /dev/null
+++ b/test/Test_Zmatrix/zmatrix.dat.save
@@ -0,0 +1,8 @@
+#IC                                                       ZMATRIX_00002
+       1    2.000    0.000    0.000    0.000    0.000    0.000    0.000
+       2    1.000    2.000    0.000    0.000    1.510    0.000    0.000
+       3    6.000    1.000    2.000    0.000    1.223  120.091    0.000
+       4    7.000    6.000    1.000    2.000    1.727  179.995  -28.942
+       5    3.000    2.000    1.000    6.000    1.088  109.303  113.518
+       6    4.000    2.000    1.000    6.000    1.088  109.698 -125.442
+       7    5.000    2.000    1.000    6.000    1.090  108.799   -5.800