Hi Debarati,
Would the 'nativecontacts <
https://amberhub.chpc.utah.edu/nativecontacts/>'
command work for what you're thinking? It is a very flexible and powerful
tool although the amount of output can be overwhelming. Something like the
following:
nativecontacts ':*RNA_resids*' ':*protein_resids*' resout
*file_with_contacting_residues* byresidue map mapout *file_with_contact_map*
Best,
Gard
On Mon, Sep 15, 2025 at 1:00 PM Debarati DasGupta via AMBER <
amber.ambermd.org> wrote:
> Hi All,
>
> I am wondering if we wanted to look at per residue interactions on a per
> frame basis is there a cpptraj script to do that?
> I can separately calculate H bonds per frame but what people need are a
> visual representation of a "interactogram" Which is for this RNA say its 20
> bases people want to look at a histogram of interactions happening per
> frame per base with and without a ligand bound to it.
>
>
> How can I achieve this using cpptraj?
>
> Debarati
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Received on Mon Sep 15 2025 - 13:30:03 PDT
