Dear Sir,
I did 10 ns dynamics of the complex and one water came
between ligand and dna during equillibration and
stays there during full production.
That is why i want to calculate the binding free
energy in the presence of water molecule.
Is it possible to calcule binding free energy in the
presence of water. If possible please give some idea
about procedure.
saurabh
--- Carlos Simmerling <carlos.simmerling.gmail.com>
wrote:
> where do the waters go in the unbound state? you
> need to define that
> before you can do the calculation. otherwise it
> should be fine to do
> it this way, although you may have to check and make
> sure that the
> program you use for the solvation calculation
> supports K+. check the
> resutls carefully with that in mind.
>
> On 3/18/07, saurabh agrawal <imsam100.yahoo.co.in>
> wrote:
> > Dear Amber users,
> >
> > I want to do mmpbsa calculation for dna drug
> > interaction in the presence of one water molecule
> and
> > K+ ion at the active site.
> > Is it possible to calculate binding free energy in
> the
> > presence water and ions with mmpbsa or any other
> > method?
> >
> > Thanking you in advance.
> >
> > saurabh
> >
> >
> >
> >
>
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Received on Wed Mar 21 2007 - 06:07:07 PDT
