[gmx-users] pdb2gmx question - protonation

Justin Lemkul jalemkul at vt.edu
Sat Feb 7 03:31:55 CET 2015

On 2/6/15 9:29 PM, Agnivo Gosai wrote:
> Dear Users
> I am using the default settings for the pdb2gmx program and I leave the
> protonation of AA residues to the program.
> Can anybody tell me about the default protonation states of LYS, ASP, GLU,
> CYS or HIS employed by pdb2gmx ?
> I checked the manual but it is not explicitly mentioned. Is there any
> literature available. I am sorry if I am asking for too much.

It is explained by reading pdb2gmx -h.  The default protonation states for all 
titratable residues are listed.  Histidine protonation is determined by 
proximity of groups that can participate in hydrogen bonding.



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