On Thu, 2015-07-09 at 20:46 -0600, Ahmed Ayoub wrote:
> Dear Amber Users,
>
> When I calculate the average ESURF term from the intermediary output files
> "_MMPBSA_receptor_gb.mdout.* ....etc" I get a value that is different from
> the average ESURF value given in the final output file. The difference is
> usually small but I don't get any difference when I do the same for other
> energy components (vdw, GB...etc). Am I missing something? Do the values
> given in the intermediary files correspond to the SASA thus need to be
> multiplied by a factor or do they correspond to the energy and should be
> used as is?
Those values are actually ignored. The surface area is computed by
cpptraj and multiplied directly by the surface tension value rather than
relying on sander's calculation. cpptraj implements both the LCPO
method (the only one really available in sander) and the molsurf method
(which is typically higher quality and *not* available in sander), so in
order to give users the choice of which radius set to use, MMPBSA.py
uses cpptraj for its ESURF calculation.
I suspect the ions may be causing your results to be a little different,
because in my tests cpptraj gave the same answers out to at least 0.01
kcal/mol.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Jul 10 2015 - 05:00:03 PDT
