Re: AMBER: Essential ions and water molecules in MMPBSA computations

From: Jiri Sponer <>
Date: Mon, 12 Mar 2007 14:05:49 +0100 (MET)

It has been done for example for quanine DNA quadruplexes,
where monovalents are essential to stabilize this DNA
It is possible and it works.

Formation pathways of a guanine-quadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates
Author(s): Stefl R, Cheatham TE, Spackova N, Fadrna E, Berger I, Koca J, Sponer J
Source: BIOPHYSICAL JOURNAL 85 (3): 1787-1804 SEP 2003

Molecular dynamics simulations of guanine quadruplex loops: Advances and force field limitations
Author(s): Fadrna E, Spackova N, Stefl R, Koca J, Cheatham TE, Sponer J
Source: BIOPHYSICAL JOURNAL 87 (1): 227-242 JUL 2004

best wishes, Jiri

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> Dear Amber community,
> I have such a complex system that one Na+ ion and two water molecules make a significant contribution to the stability of the complex and I personally wouldn't want to remove them during MMPBSA computations. I was wondering if any has succeeded including such essential ions and water molecules in MMPBSA computations. Can anyone please guide me on how this can be done and what outcome can be expected by MMPBSA for a complex system including ions and water molecules?
> My best regards,
> Jenk
> ---------------------------------
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Received on Wed Mar 14 2007 - 06:07:15 PDT
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