Dear Amber Users,
Thank you. I do not want to use this information for any other purpose. My
main purpose is to obtain the solvation free energy. Do I need to set up a
simulation in implicit solvent conditions.There were some issues related to
running PB calculations as the dihedral phase was zero. Can you suggest me
other alternatives.
Kirtana
On Sun, Oct 12, 2014 at 8:38 AM, David A Case <case.biomaps.rutgers.edu>
wrote:
> On Sun, Oct 12, 2014, kirtana S wrote:
> >
> > I want to calculate the solvation free energy of my solute which consists
> > of 5000 atoms. My solute is already solvated in explicit solvent. If I
> use
> > MMPBSA ,do I need to have three separate systems i.e solvent, solute and
> > solvated solute. Only after I obtain the change in free energy from all
> the
> > three states I can calculate the electrostatic contribution to solvation
> > energy. Here how can I obtain the hydrophobic contribution.
> > Is there any other method to obtain the solvation free energy.
>
> First, are you sure this is what you want to estimate? There are no
> measurements of such numbers, and not a lot you can do with the value you
> would obtain.
>
> MM/PBSA does not handle the sort of calculation you have in mind. You
> could
> get a quick estimate of the solvation free energy by carrying out a PB
> calculation; (if the molecule is floppy, you probably need to average
> results
> over a set of representative solute conformations).
>
> I don't immediately see a good way to use explicit solvent to do this.
>
> Maybe if you tell us what you hope to do with this information, people
> could
> suggest some alternate approaches.
>
> ...dac
>
>
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Received on Sun Oct 12 2014 - 13:00:02 PDT
