Re: [AMBER] conserved water in MMPBSA

From: Alessandro Contini <>
Date: Fri, 12 Jun 2015 15:15:56 +0200

Dear Albert,
take a look to
It might answer your question ;-)



Il 12/06/2015 15:03, Albert ha scritto:
> 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
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Alessandro Contini, PhD
Dipartimento di Scienze Farmaceutiche
Sezione di Chimica Generale e Organica "A. Marchesini"
Via Venezian, 21 20133 Milano
tel. +390250314480
skype alessandrocontini
Per destinare il 5x1000 all'Universita' degli Studi di Milano: indicare nella dichiarazione dei redditi il codice fiscale 80012650158.
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Received on Fri Jun 12 2015 - 06:30:08 PDT
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