1.0 Prerequisites

• CHARMM
  • http:https://charmm.chemistry.harvard.edu/
• MMTSB
  • https://github.com/mmtsb/toolset/
• MDconv
  • https://github.com/feiglab/mdconv.git
• OpenMM
  • http:https://openmm.org/
• locPREFMD
  • http:https://github.com/feiglab/locprefmd.git
• RWplus
  • http:https://zhanglab.ccmb.med.umich.edu/RW/

1.1. Getting PREFMD

• Cloning the PREFMD github repository
  • git clone https://github.com/feiglab/prefmd.git

1.2. Installing CHARMM

• You can get a detailed information at https://www.charmm.org/charmm/documentation/installation/
• To run PREFMD, you need
  • CHARMM with MPI (mendatory)
  • CHARMM with OpenMM (it is not supported by the lite version)

1.3. Setting environment variables

• You have to modify $PREFMD/scripts/prefmd.bashrc file
  • PREFMDDIR: path to the PREFMD home directory
  • MMTSBDIR: path to the MMTSBDIR home directory
  • CHARMMEXEC: path to the executable file of CHARMM compiled with MPI
  • CHARMMEXEC_OpenMM: path to the executable file of CHARMM compiled with OpenMM (leave it blank if you are using CHARMM lite version)
  • RWPLUS_HOME: path to the RWPLUS home directory
• Then, put those environments to the shell
  • source $PREFMD/scripts/prefmd.bashrc

1.4. Preparing force field files

• The scripts require force field files for protein residues, ions, and water The scripts prefmd.sh and prefmd_OpenMM.sh expect single CHARMM style topology and parameter files. Force field file names are given at the top of scripts are set to 'top.rtf' and 'par.prm'. These files are NOT provide with this distribution or with CHARMM and need to be generated.

  In principle any force field can be used but we recommend the CHARMM force field. CHARMM force field files are available from the CHARMM distribution (in the toppar directory).

  CHARMM provides protein force field files separately from water and ions. For example, the CHARMM c36 protein force field is found in the files: toppar/top_all36_prot.rtf toppar/par_all36_prot.prm

  while water and ion parameters are in a stream file: toppar/toppar_water_ions.str

  A utility (makeff.pl) is provided to combine those files and generated default files 'top.rtf' and 'par.prm'.

  In order to use other force fields the input files may need to be prepared manually and/or the prefmd.sh/prefmd_OpenMM.sh scripts may need to be modified.

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

• If you are using CHARMM full version and have compiled with OpenMM, then use $PREFMDDIR/scripts/prefmd.sh
  • $PREFMDDIR/scripts/prefmd.sh [options] [INPUT PDB] > [REFINED PDB]
• If you are using CHARMM lite version or want to use a simplified version of CASP13 protocol with flat-bottom harmonic restraint, then use $PREFMDDIR/scripts/prefmd_OpenMM.sh
  • $PREFMDDIR/scripts/prefmd_OpenMM.sh [options] [INPUT PDB] > [REFINED PDB]
• List of options
  • -c/--cpus: Number of CPUs to be used (default: 8)
  • -g/--gpu : GPU ID to be used (default: 0)
  • --mdsteps: Number of MD steps for each MD trajectories (default: 15000000 (30ps))
  • --mdruns : Number of MD trajectories to be generated (default: 5)
  • --tmpdir : Temporary directory path to store generated files
  • --kcons : Force constant for positional restraints (default: 0.05 kcal/mol/A^2)
  • --flat_bottom: Width of a restraint-free region for flat-bottom harmonic restraints. (optional)
    The PREFMD will run with a simplified version of CASP13 protocol (recommended value is 4.0), if it is provided.

• May, 2019: Updated to support flat-bottom harmonic restraint (--flat_bottom)
• Jul, 2017: The first release of PREFMD

• L. Heo and M. Feig, PREFMD: a web server for protein structure refinement via molecular dynamics simulations, Bioinformatics (2018) 34, 1063-1065.

• [email protected]