Subject: Re: CCL:CHARMM/Amber File Conversion

From: [email-masked] (David Case)
Date: Mon, 3 Oct 94 08:10:32 PDT

Barry Hardy <[email-masked]> wrote:

>     Can anyone suggest a program/tool that can convert CHARMM input
> files (coordinates, parameters, topology) to Amber and vice-versa?
> If not, what is the most efficient work-around?

I've worked on converting CHARMM input files into AMBER format, but it's not
easy.  Here are some of the issues you will face:

(1) The CHARMM energy function includes Urey-Bradley interactions (1-3 "bonds")
and a different way of maintaining planarity about trigonal centers than
amber does, so you will have to modify the AMBER code to include the new
functionality.

(2) CHARMM uses four-letter codes to indicate atom types, but AMBER 
allows only two-letter codes, so you will have to make a mapping of these codes.

(3) CHARMM force fields before about version 22 only used some of the torsion
angles in a molecule in the force field.  Adapting to this would require
more changes to the AMBER code, which I never attempted, but which probably
would not be too hard.

(4) CHARMM generally handles the cut-off of non-bonded forces in a different
way than AMBER, so that if you really want to reproduce the CHARMM force
field inside amber, more code modifications are required.

But the good news is that it mosly can be done.  Here's what I did:

(a) made the mapping of item (2) above, and the code changes in item (1);

(b)  edited the "all.in" file in AMBER to make the atom types and
charges correspond to those in charmm.  The atom types can be handled with
a "sed"-script, but I ended up doing the charges by hand, although it would
probably be possible to automate that as well.

(c) wrote a perl script to convert CHARMM parameter and topology files into
an AMBER "parm.dat" file.  This code is pretty well commented, but was not
written with distribution to other users in mind.

I am happy to provide those interested a copy of the perl script.  The output
files it produces contain information covered by a license agreement under
which I obtained CHARMM, and is therefore not available for redistribution.
The code changes to AMBER will probably be included in the next AMBER release.
BUT, the whole thing has not yet been properly debugged and tested, so there
are a lot of caveat emptors here.

I would be interested to know if anyone has skinned this particular cat in
a different way.  I believe that the "vice-versa" part (converting AMBER
input to CHARMM) is in considerably better shape.

...hpe this helps....dave case

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David A. Case                      |  internet: [email-masked]
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