AMBER Archive (2004)

Subject: RE: AMBER: Trajectory file conversion between Amber & Charmm

From: Thomas E. Cheatham, III (cheatham_at_chpc.utah.edu)
Date: Mon Sep 20 2004 - 13:18:46 CDT

> To do analysis on Charmm trajectories, I need the Charmm topology and
> parameter files. I already have the these files in Amber format,
> therefore the question lies in how to convert these files into Charmm
> format. Does anyone have a clue?

At present, there is no automatic conversion tool that I am aware of that
will convert between an AMBER prmtop file and a CHARMM PSF file (nor a
converter to CHARMM .rtf/.par files). Therefore you will have to use
CHARMM to build the AMBER-equivalent PSF file. This will be tricky since
you need a 1-1 mapping of atoms to have the trajectory make sense.
Although .rtf and .par files do exist for CHARMM that implement the
Cornell et al. force field, there is not a 1-1 mapping between the atoms.
You may be better off (a) reimplementing the trajectory analysis in AMBER
or ptraj, (b) writing a prmtop->PSF converter or, (c) writing a atom
swapping program to re-order the atoms in the trajectory to match
CHARMM or, (d) trying to force CHARMM to build a PSF that is compatible.
The latter three are likely tricky.

[An alternative is to use PDB files, i.e. convert the trajectory to PDB
files and then use CHARMM to load up the PDB files w/ the appropriate PSF
file; it is also possible in read in a "user specified" file format (with
some work in the COOR command) in CHARMM; if you are simply using an
external program that expects to read a CHARMM PSF and trajectory file,
you are out of luck at present.]

\ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy, Depts of
| Medicinal Chemistry and of Pharmaceutics and Pharmaceutical Chemistry
| Adjunct Asst Prof of Bioengineering; Center for High Performance Computing
| University of Utah, 30 South 2000 East, Skaggs 201, Salt Lake City, UT 84112
|
| tec3_at_utah.edu (801) 587-9652; FAX: (801) 585-9119
\ BPRP295A / INSCC 418 http://www.chpc.utah.edu/~cheatham

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