Re: [AMBER] conserved water in MMPBSA

From: George Tzotzos <>
Date: Fri, 12 Jun 2015 16:31:38 +0300

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.



> On 12 Jun 2015, at 16:03, Albert <> wrote:
> Hello:
> I've got a question about conserved water in MMPBSA calculation.
> Sometimes in the protein/ligand system there are 1-2 conserved water
> mediating the interaction between protein and ligand, and I am just
> wondering shall we keep those water molecules "explicitly" during MMPBSA
> calculation? In this case, we treat them as a part of protein instead of
> strip them off from the calculation system.
> Does anybody have any idea is it necessary to do so? If we do this, will
> this increase the accuracy of our calculation?
> thx a lot
> Albert
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Fri Jun 12 2015 - 07:00:03 PDT
Custom Search