Jaime,
you could use the "lie" (linear interaction energy) command in cpptraj
to compute interaction energies (vdw, ele) between two masks on the
atomic level. Thus, you could compute the interaction energy of your
complete ligand and a subset of its atoms with the protein.
(Although I haven't done this before with atom-based masks, the manual
suggests that it will work.)
Maybe this helps.
Best,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
Am 21.12.2023 um 11:59 schrieb VERONICA MARTIN HERNANDEZ via AMBER:
> Hi
> You can calculate the total contributions to the Gibbs energy with the AMBER module MMGBSA.py and also the contribution of each residue.
> There is a tutorial in AMBER web page
>
> I hope it helps
>
> ________________________________
> De: Jaime Rubio Martinez via AMBER <amber.ambermd.org>
> Enviado: jueves, 21 de diciembre de 2023 11:38
> Para: amber.ambermd.org <amber.ambermd.org>
> Asunto: [AMBER] ligand-protein interaction
>
>
> Hello,
> I have a ligand-protein pose and I and I would like to know the contribution of a part of the ligand (a benzene) to the interaction energy (vdw+elec).
> It's possible with Amber?
> Jaime
>
>
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Received on Thu Dec 21 2023 - 09:00:03 PST
