FWIW, you can do this calculation by adding the ‘--polarDecomp’ flag in rism3d.snglpnt or ‘polardecomp=1’ for sander.
Tyler
> On Jul 27, 2018, at 7:05 AM, Leena Aggarwal <leena.hrc.gmail.com> wrote:
>
> Thanks for the reply.
> I will try according to your suggestion.
>
> On Fri, Jul 27, 2018 at 5:55 PM, David A Case <david.case.rutgers.edu>
> wrote:
>
>> On Sat, Jul 21, 2018, Leena Aggarwal wrote:
>>>
>>> I was able to find the partial molar volume of a real protein through
>>> rism3d.snglpnt in AMBER.
>>> Can anyone suggest how we can find the partial molar volume of
>> hypothetical
>>> protein molecule without atomic charges?? I mean how to switch off the
>>> electrostatic interaction term?
>>
>> Why not the "straightforward" method of just setting all the protein
>> charges to zero, and re-running rism3d.snglpnt? This is what we do for
>> energies (in trying to get a partioning of solvation free energies into
>> polar and non-polar parts.) You might learn something about partial
>> molar volumes in the same way.
>>
>> ....dac
>>
>>
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Received on Fri Jul 27 2018 - 10:00:01 PDT
