[gmx-users] charmm to gromacs
jalemkul at vt.edu
Tue Dec 2 02:30:22 CET 2014
On 12/1/14 10:49 AM, Rebeca García Fandiño wrote:
> Dear users,
> I am trying to generate .itp files for simulating a small molecule in GROMACS using the CHARMM force field.
> Starting from a pdb, and using MATCH
> MATCH.pl -forcefield top_all36_cgenff test.pdb
> I obtain 3 files: test.rtf, top_test.rtf and test.prm
> From these files, I would like to obtain the .itp files for gromacs, and for that, I have tested the sript "charmm2gromacs-pvm.py"
> ./charmm2gromacs-pvm.py test.prm top_test.rtf
> This created a folder called cgenff-2b7.ff with 6 files:
> aminoacids.rtp atomtypes.atp ffbonded.itp ffnonbonded.itp forcefield.doc forcefield.itp
> However, these files are empty :-(
> Could anyone help me, please?
I have no idea what MATCH.pl is, but verify first that its output is sensible
and properly formatted.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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