Re: [AMBER] mmpbsa on charged sytem

From: Thomas Cheatham <>
Date: Tue, 5 Aug 2014 09:24:41 -0600 (MDT)

> 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...


"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
Received on Tue Aug 05 2014 - 08:30:02 PDT
Custom Search