[gmx-users] introduce Fluor as a accepotor in calculating hbonds

Justin Lemkul jalemkul at vt.edu
Thu Aug 13 13:58:11 CEST 2015

On 8/13/15 4:50 AM, nazli kashani javid wrote:
> Hi all,
> I want to calculate occupancy of hbond for my protein, there are one type
>   modified residue in my structure (all hydrogens in leucine amino acid have
> substituted by fluor). For calculating occupancy, I used *plot_hbmap.pl
> <http://plot_hbmap.pl>*. unfortunately F didn't report as an acceptor or
> donor in my output.dat file. so Is there any way to introduce F as an
> acceptor?

The atoms that can serve as donors and acceptors are hard-coded, so you have to 
modify the source code and recompile/reinstall to add any new species as acceptors.



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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