Are you sure you are looking at the total deltaG values for the decomposed
backbone? The gas phase energies, for instance, should cancel each other
out and give a zero contribution. But I would expect the decomp energies
for the backbone amino acids to have some contribution to the calculated
deltaG.
-Bill
On Wed, Aug 17, 2022 at 7:25 AM Miroslav Suruzhon via AMBER <
amber.ambermd.org> wrote:
> Hello,
>
> I’m running MMPBSA decomposition using MMPBSA.py which runs successfully
> using complex, receptor, and ligand .prmtop files. However, I noticed that
> although the decomposition is successful for the side chains the backbone
> contribution for all residues are set to zero. Is there any reason for
> this? My input file is below:
>
> |Input file:
> |--------------------------------------------------------------
> |&general
> |startframe=100, endframe=10000, interval=100
> |verbose = 1,
> |/
> |&pb
> |fillratio = 4.0, radiopt = 0,
> |/
> |&decomp
> |idecomp = 2,
> |dec_verbose = 3,
> |print_res = ‘1, 2, ‘,
> |/
>
> Many thanks for the help.
>
> Kind regards,
> Miro
>
> Miroslav Suruzhon MSc PhD
> Molecular Dynamics Research Scientist
> +44 (0) 7719 025700
> Exscientia
>
> The Schrödinger Building, Heatley Road, Oxford Science Park, Oxford, OX4
> 4GE
>
>
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Bill Miller III
Assistant Professor of Chemistry
Truman State University
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Received on Thu Aug 18 2022 - 14:00:09 PDT
