Re: AMBER: MMPBSA with water molecule in active site

From: Carlos Simmerling <>
Date: Sun, 18 Mar 2007 13:43:44 -0400

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 <> 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 - 06:07:06 PDT
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