Help with Topology and Parameter Files

Hello all,

I'm currently trying to set up a protein simulation in LAMMPS. While the charmm2lammps tools included with the code are sufficient to set up most of what I need, there is a slight problem. Namely, the parameters and topology for the prosthetic groups of the protein which I'm interested in are contained in an older set of XPLOR files. I was wondering if there was an easy way to convert these files to CHARMM style so I could use charmm2lammps directly?

Alternatively, is there a tool for using XPLOR formatted files to generate LAMMPS input and data files for molecules? If something like the latter existed, I would also need a way to use two different sets of top/parm files - one for the protein backbone, and another for the prosthetic groups.

Any suggestions would be appreciated, since otherwise I'm having to consider writing parser code to handle the conversions myself.

Thanks,
Thomas Allen

I’m not familar with the format of XPLOR files, maybe

someone else on the mail list is.

If you have another MD program that reads XPLOR files

and can output another format that LAMMPS can

pre-process (e.g. charmm2lamps, msi2lmp, amber2lmp),

then that would be an option.

Steve

I see. I could probably get VMD to read from the topology file, but I suppose my question is
whether or not I need the top and rtf files themselves in CHARMM format. The interface to charmm2lammps seems to suggest that it uses all four (pdb, psf, top, rtf) to generate the results,
and all the tools I’ve been able to find so far can only generate psf files; they don’t seem to know anything about the top or rtf directly.

I see. I could probably get VMD to read from the topology file, but I
suppose my question is
whether or not I need the top and rtf files themselves in CHARMM format. The
interface to charmm2lammps seems to suggest that it uses all four (pdb, psf,
top, rtf) to generate the results,
and all the tools I've been able to find so far can only generate psf files;
they don't seem to know anything about the top or rtf directly.

parameter and topology files are usually well commented and the file
formats rather obvious or documented. NAMD for example has a tutorial
on modifying topologies and adapting parameters. i think with some
common sense, a text editor and some careful debugging on very small
test systems, it should be possible to translate those manually.
remember, that you only need to convert those once and can re-use them
over and over again. :wink:

axel.