Hi all
Just picking in on the subject since i was wondering something similar:
If you call for specific donor/acceptormask you will still get an output
for each possible individual H-bond if i'm not mistaken. Would it be
possible to group H-bonds between the residues automatically so one could
say that there is A hydrogen bond between the two residues of interest in a
frame of the trajectory?
Kind regards
Charles-Alexandre Mattelaer
Op 29 dec. 2017 2:51 p.m. schreef "Daniel Roe" <daniel.r.roe.gmail.com>:
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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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>
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Received on Fri Dec 29 2017 - 06:00:05 PST
