Re: [AMBER] mmpbsa on charged sytem

From: Brian Radak <>
Date: Tue, 5 Aug 2014 10:42:00 -0400

I'm sure it's possible to do with AMBER, but maybe perhaps not with (I'm not an expert with that program and have always done my
calculations "by hand"). The hard part will be retaining the right number
of water molecules for each frame. I've not heard of retaining water in
such calculations, and without any details, I'm not sure how you would
account for them properly in the bound and unbound states. This probably
requires a survey of the literature via google or whatever other source you


On Tue, Aug 5, 2014 at 3:19 AM, Mary Varughese <> wrote:

> Sir,
> I have a nucleic acid ligand system with negatively charged ligand.
> (mimor groove binding) cooH group protrude out of the groove. i would
> like to do an mmpbsa calculation retaining certain amount of water
> shell around the complex. Is it possible to do so? is there any
> reference papers available in this regard?
> thankimg you
> mary
> _______________________________________________
> AMBER mailing list

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Received on Tue Aug 05 2014 - 08:00:03 PDT
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