have you done mm-pbsa calcualtions without including a water?
if not, you should get experience with the basic methods first.
when you do the calculation of ligand/receptor separately, you need
to think about where the water should go. that will make more sense
once you have learned basic mm-pbsa.
On 3/18/07, saurabh agrawal <imsam100.yahoo.co.in> wrote:
> 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
