[gmx-users] question about pdb2gmx
jalemkul at vt.edu
Sun Jul 13 03:30:59 CEST 2014
On 7/12/14, 7:16 PM, Tom wrote:
> Dear Gromacs Users,
> I have already prepared a protein pdb file with correct
> pronation/deprotonation state.
> How can I use pdb2gmx to generate topology file based
> on my pdb file?
You process it like any other file. If you have protonation states that differ
from pdb2gmx's assumptions (it assumes protonation states based on pH 7 and
histidine protonation based on H-bonding networks), then you can set the
appropriate forms using the appropriate command-line flags (-inter will prompt
you to choose the protonation state of every single titratable residue, but
depending on what you need to set, that may be overkill).
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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