AMBER Archive (2007)

Subject: Re: AMBER: MMPBSA with water molecule in active site

From: saurabh agrawal (imsam100_at_yahoo.co.in)
Date: Sun Mar 18 2007 - 12:30:31 CST

I did MMPBSA calcultion with Dielectric constant for
surrounding water equal to 80.
Is it not needed to worry about that particular water?

I think I sould be soory for this question.

--- Carlos Simmerling <carlos.simmerling_at_gmail.com>
wrote:

> 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_at_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_at_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_at_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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