[gmx-users] pdb2gmx

Justin Lemkul jalemkul at vt.edu
Wed Jun 25 12:02:33 CEST 2014

On 6/25/14, 4:44 AM, mirko busato wrote:
> Thank you very much,
> In my analysis ,I would like to consider Hydrogen bonds involving S atom as well.  I think that g_hbond is not built to manage Hydrogen bonds with S.
> Do you know if there are available scripts? or Could you suggest me something to solve this problem?

g_hbond is hard-coded to deal with certain groups, so it's not very flexible. 
The workaround we've used in the past is to simply rename the S atoms of 
interest as O in the .top file, generate a .tpr with those dummy names, and run 
g_hbond using that .tpr file.



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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