Thank you for the response.
Can you please send the url link for the location of the script (to
calculate the percentage of hydrogen bond)?
Thanks,
Neha
On Sat, Mar 25, 2017 at 1:36 PM, Tasneem Kausar
wrote:
> If you want to calculate hydrogen bond invloving residue there are two
> steps
> Fro
If you want to calculate hydrogen bond invloving residue there are two steps
>From gmx hbond you can obtain an xpm file where hydrogen bond existance mad
is plotted. Then calculate the percentage of hydrogen bond involving
residues from script given by justin.
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Hi,
Thank you for the reply.
Actually, we get the number of hydrogen bonds in .xvg file using
gmx hbond -s prd.tpr -f prd.xtc -n index.ndx -num hbnum.xvg
.
Can we generate an output file similar to that, which prints the bonding
residues of protein and ligand?
Thanks,
Neha
On Fri, Mar 24,
Dear Neha,
Gromacs doesn’t offer that much in terms of viewing. This sounds more like a
PyMol/VMD/Other question.
Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Department of Chemistry – BMC, Uppsala University
+46 (0)18 4
