/C36IDPSFF

CHARMM36IDPSFF force field for GROMACS

CHARMM36IDPSFF force field for GROMACS

Introduction

This is the description of the concept and the usage of CHARMM36IDPSFF force field

Recently, we developed a residue-specific force field based on CHARMM36m force field with
modified dihedral energy correlation map (CMAP) to simulate intrinsically disordered proteins (IDPs).
You can use this force field in your research according to the following information.

Usage

  1. Enter the c36IDPSFF directory and you will find the force field files

    $ cd c36IDPSFF/
    $ ls
    charmm36IDPSFF.ff test

  2. Copy the force field charmm36IDPSFF.ff to your Gromacs force field directory

    $ cp -r charmm36IDPSFF.ff/ $GROMACS/share/gromacs/top

    [Note： $GROMACS is the directory where you install the Gromacs software.]
    If you are neither a root user nor sudoer, and you have no permission to copy this folder
    to $GROMACS/share/gromacs/top, you can put them into the place where you prepare
    the .top and .gro files for simulation instead.

    Example:
    $ cp -r charmm36IDPSFF.ff/ test/
    $ cd test/
    $ gmx pdb2gmx -f test.pdb -o test.gro -water tip3p -p test.top -i test.itp -ignh
    ...
    Select the Force Field:
    From current directory:
    1: CHARMM36IDPSFF all-atom force field (April 2018)
    From $GROMACS/share/gromacs/top
    2: AMBER03 force field (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
    3: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
    ...
    [You can choose our force field by inputting "1" and then click "Enter"]

Reference

When you publish or report results using CHARMM36IDPSFF force field, please cite the following papers

  • H. Liu, D. Song, H. Lu, R. Luo and H. F. Chen. Intrinsically Disordered Protein Specific
    Force Field CHARMM36IDPSFF, Chemical Biology & Drug Design, 2018, 92, 1722-1735.
  • H. Liu, D. Song, Y. Zhang, S. Yang, R. Luo and H. F. Chen. Extensive tests and evaluation
    of the CHARMM36IDPSFF force field for intrinsically disordered proteins and folded proteins,
    Physical Chemistry Chemical Physics, 2019, 21, 21918-21931