Quickstart

Obtaining the force field files

The project is hosted on Gitlab. The most recent version, including this documentation, obtainable from there.

The preferred way to download the files is cloning the repository using git:

$ git clone https://gitlab.com/awacha/charmm-beta.ff.git charmm-beta.ff

This way the force field files can always be updated to the newest version with:

$ cd charmm-beta.ff
$ git pull origin master --tags

Versions are tagged in the repository, thus checking out a version is also straightforward:

$ cd charmm-beta.ff
$ git checkout <tag name>

The available versions can be listed:

$ cd charmm-beta.ff
$ git tag -l

Using with GROMACS

First ensure that the force field directory (charmm-beta.ff) is present as a subdirectory of any directory you intend to execute the gmx command from (either copy or more preferably, symlink).

In order to make GROMACS recognize β-amino acid residues as Protein, the contents of the residuetypes_beta.dat file in the force field directory must be appended to the residuetypes.dat file. The main file usually resides in the top directory of GROMACS (usually /usr/share/gromacs/top, or any directory pointed by the environment variable $GMXTOP). Instead of modifying this file, users are encouraged to create the updated version in their working directory (from where the gmx commands will be run). E.g.:

$ cat $GMXTOP/residuetypes.dat charmm-beta.ff/residuetypes_beta.dat > residuetypes.dat

If you have a molecular model of a β-peptide, you can create a topology with:

$ gmx pdb2gmx -f betapeptide.g96 -ff charmm-beta -ter -water -o conf.g96 -p topol.top

Generating molecular geometries

The present force field by itself does not support creating molecular geometries. However, we have made an extension to the PyMOL molecular graphics system which is able to build β-peptides in various conformations. You can find its documentation at https://pmlbeta.readthedocs.io.

Using with CHARMM

To be done…