[gmx-users] Regarding topology...
jalemkul at vt.edu
Mon Jan 16 19:49:30 CET 2017
On 1/16/17 2:44 AM, Dilip H N wrote:
> My questions are..
> 1] how to create a topology file for ammonia.??
> 2] how to create a force field for ammonia, what is the residue name for
> ammonia in .pdb file.??
> 3] Why ammonia.itp is not there in gromacs..??
> 4] Which force field to choose for ammonia..??
The CHARMM General Force Field (CGenFF) supports ammonia. Its residue name is
AMM1 and it is in our CHARMM36 port for GROMACS. Use pdb2gmx on a suitably
named coordinate file and you've got your 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
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