Hi,
As Elvis mentioned, you need to use 'hbond' analysis. To get the
number of solvent-solute hydrogen bonds vs time (data set aspect [UV])
for specific residues you'll need one entry for each residue; the
output can be redirected to one file. For example:
hbond Res12 :12 solventacceptor :WAT.O solventdonor :WAT
hbond Res15 :15 solventacceptor :WAT.O solventdonor :WAT
hbond Res21 :21 solventacceptor :WAT.O solventdonor :WAT
create numUV.agr *[UV]
To get the average for each set use the 'avg' analysis:
avg name AvgHB out AvgUV.dat *[UV]
Hope this helps,
-Dan
On Tue, Jun 6, 2017 at 8:02 AM, Saman Yousuf ali
<saman.yousufali64.yahoo.com> wrote:
> Dear all,I would like to plot a figure like the attached (average number of hydrogen bonds between ligand and water) using cpptraj. Anyone can help me out?
> Thanks
> Best, Saman Yousuf Ali
>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Tue Jun 06 2017 - 05:30:05 PDT
