locprefmd

local geometry protein structure refinement via MD

1. Installation

1.0 Prerequisites

• CHARMM
  • http://charmm.chemistry.harvard.edu/
• MMTSB
  • https://github.com/mmtsb/toolset/
• MolProbity
  • https://github.com/rlabduke/MolProbity
  • Note: requires Java and php

1.1 Getting locPREFMD

• Cloning the locPREFMD github repository
  • git clone https://github.com/feiglab/locprefmd.git

1.2 Setting environment variables

• You have to set the following environment variables:
  • MMTSBDIR: path to the MMTSBDIR home directory
  • CHARMMEXEC: path to the executable file of CHARMM
  • CHARMMDATA: path to the 'toppar' directory that comes with the CHARMM distribution
  • MOLPROBITY: path to the top of the MolProbity tree
  • LOCPREFMD: path to the locPREFMD github repository after checking out

1.3 Preparing CHARMM

• Compile a full version of CHARMM (a 'lite' version will not work)

• There is a duplicate angle in the protein parameter file that comes with CHARMM that is causing problems with recent versions of CHARMM. You may see the following error message:

  PARRDR> Error: Repeated ANGLE parameter ( 82567): NH2 CT2 CD

• If you get the above error, edit '$CHARMMDATA/par_all36_prot.prm', find the following line and add an exclamation mark in front as below:

  !NH2 CT2 CD 50.000 107.0000 ! From ALA Dipep. NH1-CT2-C, Neutral Gly Nterminus

2. How to use locPREFMD

2.1. Prepare a input protein structure in PDB format 2.2. Run locPREFMD

• $LOCPREFMD/scripts/locprefmd.sh [INPUT PDB] > [REFINED PDB]

3. Release log

• Jul, 2017: The first release of locPREFMD

4. References

• M. Feig: Local protein structure refinement via molecular dynamics simulation with locPREFMD. J. Chem. Inf. Model. (2016) 56, 1304-1312

5. Contact

• mfeiglab@gmail.com