Re: [AMBER] conserved water in MMPBSA

From: Alessandro Contini <alessandro.contini.unimi.it>
Date: Fri, 12 Jun 2015 15:15:56 +0200

Dear Albert,
take a look to
http://pubs.acs.org/doi/abs/10.1021/ct400045d
It might answer your question ;-)

Regards

Alessandro




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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 


-- 
Alessandro Contini, PhD
Dipartimento di Scienze Farmaceutiche
Sezione di Chimica Generale e Organica "A. Marchesini"
Via Venezian, 21 20133 Milano
tel. +390250314480
e-mail alessandro.contini.unimi.it
skype alessandrocontini
http://www.scopus.com/authid/detail.url?authorId=7003441091
http://orcid.org/0000-0002-4394-8956
http://www.researcherid.com/rid/F-5064-2012
****************
Per destinare il 5x1000 all'Universita' degli Studi di Milano: indicare nella dichiarazione dei redditi il codice fiscale 80012650158.
http://www.unimi.it/13084.htm?utm_source=firmaMail&utm_medium=email&utm_content=linkFirmaEmail&utm_campaign=5xmille
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jun 12 2015 - 06:30:08 PDT
Custom Search