Re: [AMBER] Regarding MMPBSA calculation

Date: Thu, 3 Jun 2021 00:50:38 +0530

first, prepare a topology file with ion and protein then stript extra water
and ions from the trajectory. Then run script without solvated
trajectory ( do not use -sp ).

Abdul Basit
Research Fellow
School of Computational & Integrative Sciences
Jawaharlal Nehru University, New Delhi-110067

On Wed, Jun 2, 2021 at 11:15 PM Rinsha Chk <> wrote:

> Hello AMBER users,
> I am doing MMPBSA energy calculation on a protein-ligand system, where
> some structural ions are retained during the simulation (in the protein).
> And I need to retain these ions in the protein during the MMPBSA
> calculation as well. But I am not able to do so, all the ions got stripped
> during the energy calculation.
> So I would like to know how one can retain the structural ions in the
> protein during MMPBSA calculation.
> I really appreciate any help you can provide.
> Rinsha. C H
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Received on Wed Jun 02 2021 - 12:30:02 PDT
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