Hi
In PBSA calculations, did you use inp=1 or 2. If left to default (inp=1),
try setting inp=2.
Also, PBSA calculations are sensitive to internal dielectric constant,
allowed values are 1 (non-polar binding site), 2 and 4 (polar binding
site).
You could experiment with these variations.
On Thursday, August 27, 2020, Camila Clemente <camilamaraclemente.gmail.com>
wrote:
> Hi!
>
> I have made a simulation of a protein-ligand modifying the NaCl
> concentrations. The simulation with the highest salt concentration is 0.5 M
> NaCl.
> I simulated 120 ns and I am doing the calculation of MMPBSA.py every 10 ns.
>
> When comparing the results of GBSA and PBSA, they are very different. The
> result for GBSA is very encouraging (-30kcal/mol) but the result for PBSA
> (1kcal/mol) is not.
> What could be the reason for such a difference in results between the two
> techniques? Is it the solvent system?
>
> Thank you for your help
> --
> *Camila*
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>
--
Best Regards
Elvis
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Received on Thu Aug 27 2020 - 08:00:03 PDT
