[gmx-users] A simple question

Justin Lemkul jalemkul at vt.edu
Mon Apr 13 14:41:41 CEST 2015

On 4/13/15 2:29 AM, saeed poorasad wrote:
> Hi .
> Dear Gromacs users .
> Today is the first day that i am working with GROMACS .I want to have a system with one C60 and about 1000 water molecules .I tried to use pdb2gmx on C60.pdb but I got fatal error , I think the problem is because of my PDB file .I want to define C-delta atom of the aromatic tryptophan amino acid for C60 carbons and i want to use oplsaa force field.
> Can you please let me know what the problem is ?

pdb2gmx won't work.  You need to use gmx x2top or find some other tool to build 
the topology.



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


More information about the gromacs.org_gmx-users mailing list