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

geeta kant geetabinwani at gmail.com
Wed Feb 4 06:43:04 CET 2009

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.


Geeta Kant
Ph.D. student,
NIMHANS, Bangalore, India
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