Re: [AMBER] mmpbsa on charged sytem

From: Alessandro Contini <>
Date: Tue, 05 Aug 2014 18:04:49 +0200

I would add:
"Explicit Ligand Hydration Shells Improve the Correlation between
MM-PB/GBSA Binding Energies and Experimental Activities", Maffucci, I
and Contini, A, J. Chem. Theory Comput., 2013, 9 (6), pp 2706–2717

We've probably chosen the wrong title and/or keyword since nobody seems
to know the paper... ;-)

Best regards


Il 05/08/2014 17:24, Thomas Cheatham ha scritto:
>> I have a nucleic acid ligand system with negatively charged ligand.
>> (mimor groove binding) cooH group protrude out of the groove. i would
>> like to do an mmpbsa calculation retaining certain amount of water
>> shell around the complex. Is it possible to do so? is there any
>> reference papers available in this regard?
> The top three include explicit water, the bottom paper, explicit ions.
> You have to decide if you want the water on the "receptor" or "ligand" for
> the free part (we normally included water in the complex + receptor). The
> first paper has an extensive supporting information...
> --tec3
> "Molecular dynamics simulations and thermodynamics analysis of DNA-drug
> complexes. Minor groove binding between 4',6-diamidino-2-phenylindole and
> DNA duplexes in solution." Spacková N, Cheatham TE 3rd, Ryjácek F, Lankas
> F, Van Meervelt L, Hobza P, Sponer J.
> J Am Chem Soc. 2003 Feb 19;125(7):1759-69.
> "Including explicit water molecules as part of the protein structure in
> MM/PBSA calculations." Zhu YL, Beroza P, Artis DR.
> J Chem Inf Model. 2014 Feb 24;54(2):462-9.
> "MM-PBSA Captures Key Role of Intercalating Water Molecules at a
> Protein-Protein Interface." Wong S, Amaro RE, McCammon JA.
> J Chem Theory Comput. 2009 Feb 10;5(2):422-429.
> "Formation pathways of a guanine-quadruplex DNA revealed by molecular
> dynamics and thermodynamic analysis of the substates." Stefl R, Cheatham
> TE 3rd, Spacková N, Fadrná E, Berger I, Koca J, Sponer J.
> Biophys J. 2003 Sep;85(3):1787-804.
> _______________________________________________
> AMBER mailing list

Alessandro Contini, PhD
Dipartimento di Scienze Farmaceutiche
Sezione di Chimica Generale e Organica "A. Marchesini"
Via Venezian, 21 20133 Milano
tel. +390250314480
ResearcherID: F-5064-2012
skype alessandrocontini
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Received on Tue Aug 05 2014 - 09:30:02 PDT
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