Hi Bill,
I’m looking at the DELTA section of the output file (both .dat and .csv that I specify) and these show zero for all residues (a snippet is below):
DELTA,Backbone Energy Decomposition:
Frame #,Residue,Location,Internal,van der Waals,Electrostatic,Polar Solvation,Non-Polar Solv.,TOTAL
1,GLY 1,R GLY 1,0.0,0.0,0.0,0.0,0.0,0.0
1,PRO 2,R PRO 2,0.0,0.0,0.0,0.0,0.0,0.0
1,HIS 3,R HIS 3,0.0,0.0,0.0,0.0,0.0,0.0
1,MET 4,R MET 4,0.0,0.0,0.0,0.0,0.0,0.0
1,SER 5,R SER 5,0.0,0.0,0.0,0.0,0.0,0.0
Many thanks.
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
> On 18 Aug 2022, at 21:57, Bill Miller III <brmilleriii.gmail.com> wrote:
>
> 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 <mailto: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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Received on Fri Aug 19 2022 - 03:30:03 PDT
