Re: [AMBER] conserved water in MMPBSA

From: Albert <>
Date: Fri, 12 Jun 2015 16:16:56 +0200

Hi guys:

thanks a lot for such helpful informations.

My case is that those conserved water molecules tightly interact with
both protein and ligand. It won't be exchanged with bulk solvent.

I will try it

thanks again.

On 06/12/2015 03:31 PM, George Tzotzos wrote:
> For a similar situation in which HOH molecules are involved in H-bonding interactions with the ligand or bridging interactions with the ligand and receptor residues, I found a positive effect on the correlation between MMGBSA calculated delta-G(total).
> However, in my view, in order to "keep those water molecules explicitly as part of the protein” one must make sure that they do not exchange with bulk solvent. You can get an indication if this is the case or not by looking at the occupancies or half-lifes of the such H-bonds.
> Regards
> George

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Received on Fri Jun 12 2015 - 07:30:02 PDT
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