[gmx-users] g_hbond problem to select donor atoms in drug

David van der Spoel spoel at xray.bmc.uu.se
Wed Feb 4 08:13:54 CET 2009

Mark Abraham wrote:
> geeta kant wrote:
>> Dear Gromacs users,
>> I am trying to analyze hydrogen bonding between a Protein and Drug by 
>> g_hbond from .xtc and .tpr and .ndx files. I am getting expected 
>> results when the H-bond donor and the hydrogen atom is from protein 
>> while the hydrogen bond acceptor atom is in the drug. The results are, 
>> however, wrong when I am trying to look for H-bond when the donor and 
>> hydrogen atoms are from the drug molecule and acceptor atoms are in 
>> the protein.  My atom names in the drug molecule sometimes start with 
>> N or A, such as NC6 (a carbon), NN6 (a nitrogen), NH61 (a hydrogen) 
>> etc. and g_hbond is considering all these atoms as hydrogen bond 
>> acceptor.  I would appreciate if somebody  gives a hint to calculate 
>> the correct hydrogen bonds in my system.
> Apparently the heuristic for detecting H-bonding involves the atom 
> names, and ones starting with N are guessed to be nitrogen. I suggest 
> going back to your pre-grompp coordinate file, editing the atom names 
> suitably, doing the corresponding edits to the atom names in the [ 
> molecule ] section(s) of your topology. Then you can regenerate a new 
> .tpr with atom names with which g_hbond will work better. So long as the 
> order of the atoms has not changed, you can combine your new .tpr and 
> your old .xtc as inputs to g_hbond.
Yes this is primitive, but I see no other way, except specifying them 
yourselves in index groups. In theory we could use the atomumber as 
well, but only if (correct!) PDB files are used or tprs for reference.

> Mark
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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