[gmx-users] Adding hydrogen

Justin Lemkul jalemkul at vt.edu
Sun Sep 29 20:35:27 CEST 2013

On 9/28/13 9:41 PM, Abu Naser wrote:
> Hi all users,
> Is it possible to add hydrogens to some of the selected atoms in the system using pdb2gmx?

pdb2gmx is a rather complex way to do it.  g_protonate is the tool for adding 
hydrogens to a configuration, but note it can only handle PDB files at the moment.



Justin A. Lemkul, Ph.D.
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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