Hello!
Perhaps these examples will help you get started. If you do the
analysis using CPPTRAJ, you can study the H-bond interactions like:
https://amberhub.chpc.utah.edu/hydrogen-bond-analysis-within-a-protein/
and
https://amberhub.chpc.utah.edu/hydrogen-bond-analysis-between-a-protein-and-a-small-molecule/
and here is an example of one way to study stacking interactions:
https://amberhub.chpc.utah.edu/stacking-percentage-protein-ligand-complex/
Hope that helps!
Rodrigo.
On Thu, Oct 12, 2023 at 12:17 AM Steinbrecher, Thomas via AMBER
<amber.ambermd.org> wrote:
>
> Hi Sourav,
>
> I dont think anyone will be able to help without more information. What
> exactly are you trying to achieve, what have you tried so far and what
> issues did you observe? The mailing list is for discussions around running
> the Amber suite of programs, but your question is broad enough to encompass
> several PhD theses...
>
> Kind Regards,
>
> Thomas
>
> On Wed, Oct 11, 2023 at 7:02 PM Sourav Bhowmik via AMBER <amber.ambermd.org>
> wrote:
>
> > **Warning** The sender address (Sourav Bhowmik via AMBER ) can not be
> > verified, sender email address could be spoofed. Please take care to
> > proceed.
> > Dear all,
> >
> > Could you please help me to calculate intermolecular H-bonding interaction
> > and pi-pi stacking interaction among the solute?
> >
> > Regards
> > Sourav Bhowmik
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
> --
> *Dr. Thomas Steinbrecher*
> Principal Scientist CADD
>
> Roche Pharma Research and Early Development
> Roche Innovation Center Basel
> F. Hoffmann-La Roche Ltd
> Bldg. 092/3.92
> Grenzacherstrasse 124
> 4070 Basel
> Switzerland
>
> Phone +41 61 682 1319
> mailto: thomas.steinbrecher.roche.com
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Received on Thu Oct 12 2023 - 07:00:03 PDT
