[gmx-users] question about pdb2gmx

Justin Lemkul 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


More information about the gromacs.org_gmx-users mailing list