[gmx-users] g_hbond and fluor

David van der Spoel spoel at xray.bmc.uu.se
Tue Oct 13 06:52:47 CEST 2009

Alvaro Cortes wrote:
> Hi all.
> I'm new at the list so i don't know if something similar has been
> discussed before.
> I tried to search in the archives, but i can't find something similar.
> I have a doubt about g_hbond and fluor acceptors. As i can see in the
> code, no parsing of F atoms is done in search_acceptors function in
> gmx_hbond.c, so i added "|| ((*top->atoms.atomname[n])[0] == 'F') ||"
> between oxygen and nitrogen parsing. This results in an increase of
> the number of hbonds reported by the program but i dont know if this
> little change  is enough or even correct.
> Someone can bring me light in this stuff?

I think it should be correct. Obviously it would be good to be more 
flexible without the need for user programming. In some contexts one 
might want to look for C-H ... 0 bonds as well and even N-H ... Aromatic 

> Thank you in advance.
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David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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