Just run 'hbond' and explicitly specify the donors/acceptors you want
with the 'donormask' and 'acceptormask' keywords, e.g.:
hbond donormask :187.O1D,O1A,O2A acceptormask :137.OG|:116.NH2
Hope this helps,
-Dan
On Fri, Dec 29, 2017 at 8:40 AM, Rana Rehan Khalid <rrkhalid.umich.edu> wrote:
> Dear Amber Users
>
> By using CPPTRAJ I performed Hbond analysis after analysis I extracted the
> data which is more specific rather then general analysis. Now I want to
> mask only specific residues and atoms how can I mask and generate the
> gnuplot for that particular interaction for example I point out some
> interaction like
>
> HM1_187.O1D SER_137.HG SER_137.OG 31779 0.4127 2.7686 154.3986
>
> HM1_187.O1A ARG_116.HH21 ARG_116.NH2 25386 0.3297 2.9128 155.5383
>
> HM1_187.O2A ARG_116.HH21 ARG_116.NH2 15880 0.2062 2.8967 142.1341
>
> how can I mask them and get the gnuplot
>
> For Example residue HM1 have 3 O hydrogen acceptor atoms like O1D,O1A,O2A
> and I can mask HM1 as 187.O1D,O1A,O2A,O2D and SER as 137.OG
>
> But I want that capptraj show only HM1 4 O hydrogen interactions with
> specific
> SER_137.HG SER_137.OG, ARG_116.HH21 ARG_116.NH2
>
> KIndly guide how I can mask and plot the results gnuplot.
> Best Regards
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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 Fri Dec 29 2017 - 06:00:05 PST
