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…