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
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Received on Mon Jul 08 2019 - 07:00:01 PDT
