Thank you Sir
On Fri, Dec 29, 2017 at 6:58 PM, Charles-Alexandre Mattelaer <
camattelaer01.gmail.com> wrote:
> 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
> > > _______________________________________________
> > > AMBER mailing list
> > > 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
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Dec 29 2017 - 08:30:02 PST
