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.
Mark
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
