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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