I'm not totally clear on what you want to measure, do you want to measure
the binding energy for a SINGLE water molecular to your UNSOLVATED polymer
in a vacuum? MMPBSA is generally used with implicit solvent, but if you
want to use the same method and just mimic being in a vacuum, you can set
the external dielectric to 1.0, it's not the most efficient method, but it
should work.
~Aron
On Sat, Apr 7, 2012 at 1:35 AM, kirtana S <skirtana4.gmail.com> wrote:
> I want to calculate the binding of water molecules with the polymer chains
> in presence of ions and compare my results to another system without the
> presence of ions.
> Is there any utility which can help in the calculations
>
> Thanks
> Kirtana
> On Fri, Apr 6, 2012 at 9:04 PM, case <case.biomaps.rutgers.edu> wrote:
>
> > On Fri, Apr 06, 2012, kirtana S wrote:
> > >
> > > My system consists of a polymer molecule in explicit water(TIP3P) with
> > > ions. Using MMGBSA I have to use a vacuum trajectory and topology files
> > of
> > > each ligand and receptor.
> > > Now to calculate the binding free energy of solvent with the polymer
> > > molecule how should I go about.
> >
> > It's not clear what energy you want: there would not ordinarily be a
> > "binding
> > free energy" between a polymer and solvent. Or at least, you would have
> to
> > define this carefully.
> >
> > One could estimate the transfer free energy between gas phase and water,
> > which
> > would be something like a free energy of interaction between the two.
> But
> > this
> > is not often an interesting value per se, since it generally can't be
> > measured.
> >
> > ....dac
> >
> >
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--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Fri Apr 06 2012 - 23:00:03 PDT
