Thank you, Dan, it really helped.
On Mon, Jul 8, 2019 at 7:02 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> You should be able to get the information that you need with the
> 'nativecontacts' command of cpptraj, and in particular in conjunction
> with the 'mindist' keyword. If you don't care about "native" contacts
> (i.e. contacts relative to a specific reference structure) you can use
> the 'skipnative' keyword. See the manual for many more details.
>
> Hope this helps,
>
> -Dan
>
> On Mon, Jul 8, 2019 at 7:32 AM Rinsha Chk <rinshachk.gmail.com> wrote:
> >
> > Dear AMBER users,
> > I am doing 10ns MD simulation on a protein-ligand complex (using
> Amber16).
> > And I would like to know how one can determine the closest distance
> between
> > the ligand and particular residues from the MD trajectory (1000
> > snapshots), and analyze how this closest distance varies during the 10ns
> > simulation, or how many times these closest distances are revisited
> during
> > the simulation.
> >
> > Thank you
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
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>
--
Rinsha. C H
Research Scholar
Theoretical and Computational Chemistry Lab
Department of Chemistry
NIT Calicut
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Received on Tue Jul 09 2019 - 03:30:01 PDT
