Re: [AMBER] MM-PBSA free energy calculation with keeping x-ray water

From: Kenneth Huang <>
Date: Mon, 3 Aug 2015 15:57:14 -0400


You should be able to- you'll just have to be careful when making your
ligand, receptor and complex file and be careful not to strip out the water
molecules that you want to preserve, usually by renaming the water atoms to
something other than WAT.

What impact it'll have on the energy is hard to say- I've only ever seen
people keep specific water atoms for MMPBSA in DNA/RNA complexes. If
nothing else, I'd do it once without the waters, and then again with the
waters just to have a point of comparison.



On Mon, Aug 3, 2015 at 3:45 PM, bharat lakhani <> wrote:

> Dear Amber users
> Is it possible to run a MM-PBSA binding free energy calculation through
> keeping x-ray waters in the ligand file along with the ATP-MG, as they are
> important for stabilization. Thanks
> --
> regards
> Bharat Lakhani
> _______________________________________________
> AMBER mailing list

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Received on Mon Aug 03 2015 - 13:00:06 PDT
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