diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx index b676fe3513..ab71a0d6a5 100644 --- a/doc/cpptraj.lyx +++ b/doc/cpptraj.lyx @@ -15596,7 +15596,7 @@ Options for pdb format \end_layout \begin_layout LyX-Code - [include_ep] [conect] [keepext] [usecol21] + [include_ep] [conect] [conectmode ] [keepext] [usecol21] \end_layout \begin_layout LyX-Code @@ -15698,6 +15698,15 @@ include_ep Include extra points. conect Write CONECT records for all bonds. \end_layout +\begin_layout Description +conectmode +\begin_inset space ~ +\end_inset + + Write CONECT records for ='all' (all bonds), 'het' (HETATM only), + 'none' (no CONECT). +\end_layout + \begin_layout Description keepext Keep filename extension; write '..' instead (implies 'multi'). diff --git a/src/Traj_PDBfile.cpp b/src/Traj_PDBfile.cpp index 35ac3b1f99..a93b132bba 100644 --- a/src/Traj_PDBfile.cpp +++ b/src/Traj_PDBfile.cpp @@ -237,7 +237,8 @@ void Traj_PDBfile::WriteHelp() { "\tchainid : Write character 'c' in chain ID column.\n" "\tsg : Space group for CRYST1 record, only if box coordinates written.\n" "\tinclude_ep : Include extra points.\n" - "\tconect : Write CONECT records using bond information.\n" + "\tconect : Write CONECT records using bond information (if 'pdbres', only for HETATM).\n" + "\tconectmode : Write CONECT records for ='all' (all bonds), 'het' (HETATM only), 'none' (no CONECT).\n" "\tkeepext : Keep filename extension; write '..' instead (implies 'multi').\n" "\tusecol21 : Use column 21 for 4-letter residue names.\n" "\tbfacdefault <#> : Default value to use in B-factor column (default 0).\n" @@ -291,6 +292,20 @@ int Traj_PDBfile::processWriteArgs(ArgList& argIn, DataSetList const& DSLin) { conectMode_ = HETATM_ONLY; else conectMode_ = NO_CONECT; + // Override conect mode + std::string conectmode = argIn.GetStringKey("conectmode"); + if (!conectmode.empty()) { + if (conectmode == "all") + conectMode_ = ALL_BONDS; + else if (conectmode == "het") + conectMode_ = HETATM_ONLY; + else if (conectmode == "none") + conectMode_ = NO_CONECT; + else { + mprinterr("Error: Unrecognized keyword for 'conectmode': %s\n", conectmode.c_str()); + return 1; + } + } prependExt_ = argIn.hasKey("keepext"); // Implies MULTI if (prependExt_) pdbWriteMode_ = MULTI; space_group_ = argIn.GetStringKey("sg"); @@ -472,7 +487,7 @@ int Traj_PDBfile::setupTrajout(FileName const& fname, Topology* trajParm, resIsHet_.reserve( trajParm->Nres() ); ss_residues_.clear(); ss_atoms_.clear(); - if (pdbres_) { + if (pdbres_ || conectMode_ == HETATM_ONLY) { Iarray cys_idxs_; ///< Hold CYS residue indices for (Topology::res_iterator res = trajParm->ResStart(); res != trajParm->ResEnd(); ++res) @@ -536,7 +551,10 @@ int Traj_PDBfile::setupTrajout(FileName const& fname, Topology* trajParm, else if (rname[0] == 'C') rname=" DC "; } } - resNames_.push_back( rname ); + if (pdbres_) + resNames_.push_back( rname ); + else + resNames_.push_back( res->Name() ); // Any non-standard residue should get HETATM if ( rname == "CYS " ) // NOTE: Comparing to CYS works here since HETATM_ONLY is only active diff --git a/src/Version.h b/src/Version.h index e3e885103c..a1a0f1889d 100644 --- a/src/Version.h +++ b/src/Version.h @@ -12,7 +12,7 @@ * Whenever a number that precedes is incremented, all subsequent * numbers should be reset to 0. */ -#define CPPTRAJ_INTERNAL_VERSION "V4.29.6" +#define CPPTRAJ_INTERNAL_VERSION "V4.29.7" /// PYTRAJ relies on this #define CPPTRAJ_VERSION_STRING CPPTRAJ_INTERNAL_VERSION #endif diff --git a/test/Test_PDB/RunTest.sh b/test/Test_PDB/RunTest.sh index 2f1cfbc304..03e85f95de 100755 --- a/test/Test_PDB/RunTest.sh +++ b/test/Test_PDB/RunTest.sh @@ -4,7 +4,7 @@ CleanFiles pdb.in test.pdb tz2.pqr.gb.pdb tz2.pqr.parse.pdb \ tz2.pqr.vdw.pdb chainA.dat oresnum.dat tz2.plain.pdb \ - 2b5t.fromparm.pdb altloca.pdb + 2b5t.fromparm.pdb altloca.pdb tz2.het.pdb INPUT="-i pdb.in" @@ -40,12 +40,14 @@ trajout tz2.pqr.parse.pdb parse # PARSE radii trajout tz2.pqr.vdw.pdb dumpr* # VDW radii # Test default chain ID write trajout tz2.plain.pdb pdbres +trajout tz2.het.pdb conectmode het EOF RunCpptraj "$UNITNAME" DoTest tz2.pqr.gb.pdb.save tz2.pqr.gb.pdb DoTest tz2.pqr.parse.pdb.save tz2.pqr.parse.pdb DoTest tz2.pqr.vdw.pdb.save tz2.pqr.vdw.pdb DoTest tz2.plain.pdb.save tz2.plain.pdb + DoTest tz2.het.pdb.save tz2.het.pdb fi } diff --git a/test/Test_PDB/tz2.het.pdb.save b/test/Test_PDB/tz2.het.pdb.save new file mode 100644 index 0000000000..3799779c36 --- /dev/null +++ b/test/Test_PDB/tz2.het.pdb.save @@ -0,0 +1,231 @@ +ATOM 1 N SER 1 -1.889 9.159 7.569 1.00 0.00 N +ATOM 2 H1 SER 1 -1.037 8.691 7.296 1.00 0.00 H +ATOM 3 H2 SER 1 -1.900 9.298 8.569 1.00 0.00 H +ATOM 4 H3 SER 1 -2.538 8.447 7.265 1.00 0.00 H +ATOM 5 CA SER 1 -2.064 10.501 6.993 1.00 0.00 C +ATOM 6 HA SER 1 -3.100 10.824 7.102 1.00 0.00 H +ATOM 7 CB SER 1 -1.230 11.561 7.707 1.00 0.00 C +ATOM 8 HB2 SER 1 -1.670 11.811 8.673 1.00 0.00 H +ATOM 9 HB3 SER 1 -1.248 12.503 7.159 1.00 0.00 H +ATOM 10 OG SER 1 0.123 11.216 7.904 1.00 0.00 O +ATOM 11 HG SER 1 0.274 11.728 8.701 1.00 0.00 H +ATOM 12 C SER 1 -1.613 10.418 5.542 1.00 0.00 C +ATOM 13 O SER 1 -2.498 10.433 4.689 1.00 0.00 O +ATOM 14 N TRP 2 -0.366 10.572 5.090 1.00 0.00 N +ATOM 15 H TRP 2 0.344 10.612 5.808 1.00 0.00 H +ATOM 16 CA TRP 2 0.195 10.697 3.760 1.00 0.00 C +ATOM 17 HA TRP 2 -0.218 11.569 3.254 1.00 0.00 H +ATOM 18 CB TRP 2 1.710 10.879 3.709 1.00 0.00 C +ATOM 19 HB2 TRP 2 2.208 9.986 4.087 1.00 0.00 H +ATOM 20 HB3 TRP 2 1.927 11.641 4.458 1.00 0.00 H +ATOM 21 CG TRP 2 2.265 11.291 2.384 1.00 0.00 C +ATOM 22 CD1 TRP 2 2.032 12.500 1.827 1.00 0.00 C +ATOM 23 HD1 TRP 2 1.538 13.333 2.305 1.00 0.00 H +ATOM 24 NE1 TRP 2 2.860 12.580 0.724 1.00 0.00 N +ATOM 25 HE1 TRP 2 2.929 13.404 0.143 1.00 0.00 H +ATOM 26 CE2 TRP 2 3.662 11.460 0.646 1.00 0.00 C +ATOM 27 CZ2 TRP 2 4.620 11.160 -0.330 1.00 0.00 C +ATOM 28 HZ2 TRP 2 5.059 11.863 -1.023 1.00 0.00 H +ATOM 29 CH2 TRP 2 5.091 9.843 -0.377 1.00 0.00 C +ATOM 30 HH2 TRP 2 5.854 9.610 -1.105 1.00 0.00 H +ATOM 31 CZ3 TRP 2 4.545 8.850 0.445 1.00 0.00 C +ATOM 32 HZ3 TRP 2 4.823 7.840 0.182 1.00 0.00 H +ATOM 33 CE3 TRP 2 3.549 9.159 1.379 1.00 0.00 C +ATOM 34 HE3 TRP 2 3.135 8.430 2.059 1.00 0.00 H +ATOM 35 CD2 TRP 2 3.075 10.477 1.483 1.00 0.00 C +ATOM 36 C TRP 2 -0.190 9.609 2.768 1.00 0.00 C +ATOM 37 O TRP 2 -0.452 9.963 1.621 1.00 0.00 O +ATOM 38 N THR 3 -0.268 8.402 3.334 1.00 0.00 N +ATOM 39 H THR 3 -0.260 8.275 4.336 1.00 0.00 H +ATOM 40 CA THR 3 -0.606 7.172 2.647 1.00 0.00 C +ATOM 41 HA THR 3 -0.180 7.266 1.648 1.00 0.00 H +ATOM 42 CB THR 3 -0.093 5.992 3.468 1.00 0.00 C +ATOM 43 HB THR 3 -0.586 5.081 3.128 1.00 0.00 H +ATOM 44 CG2 THR 3 1.343 5.648 3.081 1.00 0.00 C +ATOM 45 HG21 THR 3 1.306 5.005 2.202 1.00 0.00 H +ATOM 46 HG22 THR 3 1.955 6.543 2.967 1.00 0.00 H +ATOM 47 HG23 THR 3 1.828 5.068 3.866 1.00 0.00 H +ATOM 48 OG1 THR 3 -0.273 6.246 4.843 1.00 0.00 O +ATOM 49 HG1 THR 3 0.428 5.750 5.271 1.00 0.00 H +ATOM 50 C THR 3 -2.073 6.882 2.363 1.00 0.00 C +ATOM 51 O THR 3 -2.884 6.685 3.265 1.00 0.00 O +ATOM 52 N TRP 4 -2.414 6.796 1.075 1.00 0.00 N +ATOM 53 H TRP 4 -1.631 6.756 0.439 1.00 0.00 H +ATOM 54 CA TRP 4 -3.689 6.286 0.613 1.00 0.00 C +ATOM 55 HA TRP 4 -4.288 6.020 1.485 1.00 0.00 H +ATOM 56 CB TRP 4 -4.465 7.275 -0.253 1.00 0.00 C +ATOM 57 HB2 TRP 4 -5.450 6.821 -0.366 1.00 0.00 H +ATOM 58 HB3 TRP 4 -4.022 7.162 -1.242 1.00 0.00 H +ATOM 59 CG TRP 4 -4.632 8.723 0.077 1.00 0.00 C +ATOM 60 CD1 TRP 4 -3.902 9.713 -0.483 1.00 0.00 C +ATOM 61 HD1 TRP 4 -3.089 9.553 -1.176 1.00 0.00 H +ATOM 62 NE1 TRP 4 -4.473 10.923 -0.141 1.00 0.00 N +ATOM 63 HE1 TRP 4 -4.136 11.861 -0.306 1.00 0.00 H +ATOM 64 CE2 TRP 4 -5.469 10.746 0.798 1.00 0.00 C +ATOM 65 CZ2 TRP 4 -6.330 11.693 1.365 1.00 0.00 C +ATOM 66 HZ2 TRP 4 -6.276 12.746 1.130 1.00 0.00 H +ATOM 67 CH2 TRP 4 -7.374 11.196 2.154 1.00 0.00 C +ATOM 68 HH2 TRP 4 -8.230 11.822 2.362 1.00 0.00 H +ATOM 69 CZ3 TRP 4 -7.630 9.824 2.259 1.00 0.00 C +ATOM 70 HZ3 TRP 4 -8.379 9.482 2.959 1.00 0.00 H +ATOM 71 CE3 TRP 4 -6.776 8.905 1.638 1.00 0.00 C +ATOM 72 HE3 TRP 4 -6.974 7.872 1.884 1.00 0.00 H +ATOM 73 CD2 TRP 4 -5.703 9.347 0.848 1.00 0.00 C +ATOM 74 C TRP 4 -3.632 4.926 -0.068 1.00 0.00 C +ATOM 75 O TRP 4 -4.279 3.952 0.309 1.00 0.00 O +ATOM 76 N GLU 5 -2.795 4.872 -1.106 1.00 0.00 N +ATOM 77 H GLU 5 -2.278 5.708 -1.339 1.00 0.00 H +ATOM 78 CA GLU 5 -2.535 3.723 -1.950 1.00 0.00 C +ATOM 79 HA GLU 5 -3.007 2.948 -1.346 1.00 0.00 H +ATOM 80 CB GLU 5 -3.413 3.524 -3.183 1.00 0.00 C +ATOM 81 HB2 GLU 5 -3.139 4.141 -4.038 1.00 0.00 H +ATOM 82 HB3 GLU 5 -4.386 3.787 -2.767 1.00 0.00 H +ATOM 83 CG GLU 5 -3.470 2.108 -3.748 1.00 0.00 C +ATOM 84 HG2 GLU 5 -2.447 1.793 -3.953 1.00 0.00 H +ATOM 85 HG3 GLU 5 -4.039 2.425 -4.623 1.00 0.00 H +ATOM 86 CD GLU 5 -4.189 1.123 -2.837 1.00 0.00 C +ATOM 87 OE1 GLU 5 -3.803 0.771 -1.702 1.00 0.00 O +ATOM 88 OE2 GLU 5 -5.263 0.601 -3.207 1.00 0.00 O +ATOM 89 C GLU 5 -1.058 3.518 -2.255 1.00 0.00 C +ATOM 90 O GLU 5 -0.301 4.414 -2.619 1.00 0.00 O +ATOM 91 N ASN 6 -0.668 2.265 -2.009 1.00 0.00 N +ATOM 92 H ASN 6 -1.323 1.656 -1.539 1.00 0.00 H +ATOM 93 CA ASN 6 0.639 1.696 -2.267 1.00 0.00 C +ATOM 94 HA ASN 6 1.239 2.453 -2.772 1.00 0.00 H +ATOM 95 CB ASN 6 1.412 1.366 -0.993 1.00 0.00 C +ATOM 96 HB2 ASN 6 2.224 0.703 -1.291 1.00 0.00 H +ATOM 97 HB3 ASN 6 0.712 0.882 -0.311 1.00 0.00 H +ATOM 98 CG ASN 6 2.154 2.550 -0.391 1.00 0.00 C +ATOM 99 OD1 ASN 6 2.809 3.347 -1.058 1.00 0.00 O +ATOM 100 ND2 ASN 6 2.359 2.519 0.928 1.00 0.00 N +ATOM 101 HD21 ASN 6 1.869 1.897 1.556 1.00 0.00 H +ATOM 102 HD22 ASN 6 3.024 3.196 1.272 1.00 0.00 H +ATOM 103 C ASN 6 0.509 0.488 -3.185 1.00 0.00 C +ATOM 104 O ASN 6 -0.457 -0.250 -3.004 1.00 0.00 O +ATOM 105 N GLY 7 1.463 0.247 -4.087 1.00 0.00 N +ATOM 106 H GLY 7 2.372 0.658 -3.932 1.00 0.00 H +ATOM 107 CA GLY 7 1.399 -0.902 -4.967 1.00 0.00 C +ATOM 108 HA2 GLY 7 2.180 -0.882 -5.728 1.00 0.00 H +ATOM 109 HA3 GLY 7 0.501 -0.799 -5.576 1.00 0.00 H +ATOM 110 C GLY 7 1.448 -2.275 -4.313 1.00 0.00 C +ATOM 111 O GLY 7 0.727 -2.576 -3.364 1.00 0.00 O +ATOM 112 N LYS 8 2.361 -3.118 -4.801 1.00 0.00 N +ATOM 113 H LYS 8 3.080 -2.784 -5.426 1.00 0.00 H +ATOM 114 CA LYS 8 2.541 -4.514 -4.458 1.00 0.00 C +ATOM 115 HA LYS 8 1.627 -5.015 -4.138 1.00 0.00 H +ATOM 116 CB LYS 8 3.123 -5.283 -5.641 1.00 0.00 C +ATOM 117 HB2 LYS 8 2.435 -5.243 -6.486 1.00 0.00 H +ATOM 118 HB3 LYS 8 3.335 -6.318 -5.372 1.00 0.00 H +ATOM 119 CG LYS 8 4.416 -4.746 -6.248 1.00 0.00 C +ATOM 120 HG2 LYS 8 5.308 -4.960 -5.660 1.00 0.00 H +ATOM 121 HG3 LYS 8 4.393 -3.674 -6.439 1.00 0.00 H +ATOM 122 CD LYS 8 4.726 -5.503 -7.536 1.00 0.00 C +ATOM 123 HD2 LYS 8 3.992 -5.272 -8.308 1.00 0.00 H +ATOM 124 HD3 LYS 8 4.584 -6.543 -7.241 1.00 0.00 H +ATOM 125 CE LYS 8 6.148 -5.338 -8.066 1.00 0.00 C +ATOM 126 HE2 LYS 8 6.521 -6.290 -8.444 1.00 0.00 H +ATOM 127 HE3 LYS 8 6.848 -5.025 -7.290 1.00 0.00 H +ATOM 128 NZ LYS 8 6.177 -4.420 -9.214 1.00 0.00 N +ATOM 129 HZ1 LYS 8 6.046 -3.547 -8.722 1.00 0.00 H +ATOM 130 HZ2 LYS 8 7.131 -4.392 -9.546 1.00 0.00 H +ATOM 131 HZ3 LYS 8 5.471 -4.550 -9.925 1.00 0.00 H +ATOM 132 C LYS 8 3.512 -4.519 -3.286 1.00 0.00 C +ATOM 133 O LYS 8 4.624 -5.042 -3.286 1.00 0.00 O +ATOM 134 N TRP 9 2.925 -4.256 -2.116 1.00 0.00 N +ATOM 135 H TRP 9 2.010 -3.879 -2.316 1.00 0.00 H +ATOM 136 CA TRP 9 3.341 -4.262 -0.728 1.00 0.00 C +ATOM 137 HA TRP 9 4.410 -4.045 -0.724 1.00 0.00 H +ATOM 138 CB TRP 9 2.625 -3.068 -0.104 1.00 0.00 C +ATOM 139 HB2 TRP 9 1.589 -3.294 0.148 1.00 0.00 H +ATOM 140 HB3 TRP 9 2.835 -2.194 -0.721 1.00 0.00 H +ATOM 141 CG TRP 9 3.288 -2.462 1.091 1.00 0.00 C +ATOM 142 CD1 TRP 9 2.925 -2.436 2.393 1.00 0.00 C +ATOM 143 HD1 TRP 9 1.949 -2.799 2.678 1.00 0.00 H +ATOM 144 NE1 TRP 9 3.855 -1.845 3.224 1.00 0.00 N +ATOM 145 HE1 TRP 9 3.885 -1.848 4.234 1.00 0.00 H +ATOM 146 CE2 TRP 9 4.827 -1.303 2.408 1.00 0.00 C +ATOM 147 CZ2 TRP 9 5.911 -0.471 2.714 1.00 0.00 C +ATOM 148 HZ2 TRP 9 6.139 -0.156 3.721 1.00 0.00 H +ATOM 149 CH2 TRP 9 6.841 -0.141 1.722 1.00 0.00 C +ATOM 150 HH2 TRP 9 7.725 0.405 2.018 1.00 0.00 H +ATOM 151 CZ3 TRP 9 6.584 -0.590 0.421 1.00 0.00 C +ATOM 152 HZ3 TRP 9 7.231 -0.235 -0.368 1.00 0.00 H +ATOM 153 CE3 TRP 9 5.424 -1.297 0.082 1.00 0.00 C +ATOM 154 HE3 TRP 9 5.139 -1.465 -0.946 1.00 0.00 H +ATOM 155 CD2 TRP 9 4.479 -1.620 1.069 1.00 0.00 C +ATOM 156 C TRP 9 2.945 -5.593 -0.105 1.00 0.00 C +ATOM 157 O TRP 9 3.022 -6.675 -0.682 1.00 0.00 O +ATOM 158 N THR 10 2.531 -5.609 1.164 1.00 0.00 N +ATOM 159 H THR 10 2.711 -4.794 1.731 1.00 0.00 H +ATOM 160 CA THR 10 2.254 -6.874 1.815 1.00 0.00 C +ATOM 161 HA THR 10 2.982 -7.667 1.644 1.00 0.00 H +ATOM 162 CB THR 10 2.207 -6.622 3.320 1.00 0.00 C +ATOM 163 HB THR 10 1.722 -5.667 3.526 1.00 0.00 H +ATOM 164 CG2 THR 10 1.456 -7.659 4.149 1.00 0.00 C +ATOM 165 HG21 THR 10 1.581 -7.464 5.214 1.00 0.00 H +ATOM 166 HG22 THR 10 0.402 -7.468 3.946 1.00 0.00 H +ATOM 167 HG23 THR 10 1.725 -8.640 3.755 1.00 0.00 H +ATOM 168 OG1 THR 10 3.460 -6.501 3.954 1.00 0.00 O +ATOM 169 HG1 THR 10 3.385 -6.097 4.822 1.00 0.00 H +ATOM 170 C THR 10 0.889 -7.354 1.344 1.00 0.00 C +ATOM 171 O THR 10 -0.172 -6.760 1.524 1.00 0.00 O +ATOM 172 N TRP 11 0.906 -8.522 0.699 1.00 0.00 N +ATOM 173 H TRP 11 1.723 -9.115 0.734 1.00 0.00 H +ATOM 174 CA TRP 11 -0.188 -9.066 -0.080 1.00 0.00 C +ATOM 175 HA TRP 11 -0.737 -8.220 -0.495 1.00 0.00 H +ATOM 176 CB TRP 11 0.412 -10.010 -1.117 1.00 0.00 C +ATOM 177 HB2 TRP 11 1.113 -10.710 -0.661 1.00 0.00 H +ATOM 178 HB3 TRP 11 0.887 -9.368 -1.859 1.00 0.00 H +ATOM 179 CG TRP 11 -0.539 -10.928 -1.816 1.00 0.00 C +ATOM 180 CD1 TRP 11 -1.313 -10.686 -2.898 1.00 0.00 C +ATOM 181 HD1 TRP 11 -1.337 -9.764 -3.460 1.00 0.00 H +ATOM 182 NE1 TRP 11 -1.971 -11.786 -3.411 1.00 0.00 N +ATOM 183 HE1 TRP 11 -2.384 -11.864 -4.330 1.00 0.00 H +ATOM 184 CE2 TRP 11 -1.957 -12.763 -2.437 1.00 0.00 C +ATOM 185 CZ2 TRP 11 -2.785 -13.865 -2.191 1.00 0.00 C +ATOM 186 HZ2 TRP 11 -3.631 -14.012 -2.846 1.00 0.00 H +ATOM 187 CH2 TRP 11 -2.600 -14.709 -1.089 1.00 0.00 C +ATOM 188 HH2 TRP 11 -3.315 -15.473 -0.823 1.00 0.00 H +ATOM 189 CZ3 TRP 11 -1.518 -14.345 -0.278 1.00 0.00 C +ATOM 190 HZ3 TRP 11 -1.325 -14.936 0.604 1.00 0.00 H +ATOM 191 CE3 TRP 11 -0.809 -13.146 -0.419 1.00 0.00 C +ATOM 192 HE3 TRP 11 -0.038 -12.834 0.270 1.00 0.00 H +ATOM 193 CD2 TRP 11 -1.034 -12.259 -1.484 1.00 0.00 C +ATOM 194 C TRP 11 -1.079 -9.752 0.946 1.00 0.00 C +ATOM 195 O TRP 11 -0.710 -10.673 1.672 1.00 0.00 O +ATOM 196 N LYS 12 -2.344 -9.326 0.949 1.00 0.00 N +ATOM 197 H LYS 12 -2.456 -8.339 0.770 1.00 0.00 H +ATOM 198 CA LYS 12 -3.470 -9.926 1.636 1.00 0.00 C +ATOM 199 HA LYS 12 -3.097 -10.439 2.522 1.00 0.00 H +ATOM 200 CB LYS 12 -4.384 -8.814 2.142 1.00 0.00 C +ATOM 201 HB2 LYS 12 -5.389 -9.112 2.440 1.00 0.00 H +ATOM 202 HB3 LYS 12 -4.439 -8.009 1.409 1.00 0.00 H +ATOM 203 CG LYS 12 -3.799 -8.092 3.352 1.00 0.00 C +ATOM 204 HG2 LYS 12 -2.889 -7.566 3.064 1.00 0.00 H +ATOM 205 HG3 LYS 12 -3.691 -8.724 4.233 1.00 0.00 H +ATOM 206 CD LYS 12 -4.848 -7.024 3.650 1.00 0.00 C +ATOM 207 HD2 LYS 12 -5.691 -7.411 4.222 1.00 0.00 H +ATOM 208 HD3 LYS 12 -5.130 -6.495 2.740 1.00 0.00 H +ATOM 209 CE LYS 12 -4.108 -6.019 4.529 1.00 0.00 C +ATOM 210 HE2 LYS 12 -3.183 -5.635 4.099 1.00 0.00 H +ATOM 211 HE3 LYS 12 -3.885 -6.553 5.452 1.00 0.00 H +ATOM 212 NZ LYS 12 -4.877 -4.802 4.829 1.00 0.00 N +ATOM 213 HZ1 LYS 12 -5.132 -4.305 3.987 1.00 0.00 H +ATOM 214 HZ2 LYS 12 -5.718 -4.968 5.362 1.00 0.00 H +ATOM 215 HZ3 LYS 12 -4.250 -4.263 5.410 1.00 0.00 H +ATOM 216 C LYS 12 -4.395 -10.778 0.779 1.00 0.00 C +ATOM 217 O LYS 12 -4.483 -11.939 1.172 1.00 0.00 O +HETATM 218 N NME 13 -4.832 -10.202 -0.344 1.00 0.00 N +HETATM 219 H NME 13 -4.647 -9.239 -0.587 1.00 0.00 H +HETATM 220 CH3 NME 13 -5.720 -10.866 -1.277 1.00 0.00 C +HETATM 221 HH31 NME 13 -5.591 -11.946 -1.340 1.00 0.00 H +HETATM 222 HH32 NME 13 -6.757 -10.886 -0.942 1.00 0.00 H +HETATM 223 HH33 NME 13 -5.777 -10.358 -2.240 1.00 0.00 H +TER 224 NME 13 +CONECT 218 216 219 220 +CONECT 219 218 +CONECT 220 218 221 222 223 +CONECT 221 220 +CONECT 222 220 +CONECT 223 220 +END