[gmx-users] HBond for F and S

Justin Lemkul jalemkul at vt.edu
Mon Apr 24 21:17:16 CEST 2017

On 4/24/17 3:15 PM, Marcelo Depólo wrote:
> Hi,
> Can gmx hbond also calculates hbonds between non-canonical atoms like S or
> F as well? If so, how can I do it?

Without changing the code, the only way to do it is to rename the atoms in the 
topology as some type of oxygen, create a new .tpr file, and use that .tpr file 
for the hydrogen bond analysis.



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


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