On Fri, Dec 29, 2017 at 8:58 AM, Charles-Alexandre Mattelaer
<camattelaer01.gmail.com> wrote:
> 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?
I see, so you'd like a mode of 'hbond' where you essentially give it a
list of hydrogen bonds you would like tracked instead of a pool of
donors/acceptors, right? Some keyword like 'specific' where you would
specify the exact donor heavy atom/hydrogen and acceptor to be
tracked, e.g.
hbond specific :137.HG :137.OG :187.O1D specific :116.HH21 :116.NH2 :187.O1A ...
So currently the only way to do something like this is through a
combination of distance/angle/filter commands. However, the 'hbond'
command isn't set up to do this right now. It might be a cool feature
to add though. Thanks for the question!
-Dan
>
> 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
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
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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 Jan 02 2018 - 10:30:03 PST
