AMBER Archive (2003)

Subject: Re: mm_pbsa

From: Lepsa (lepsik_at_marilyn.uochb.cas.cz)
Date: Wed Feb 26 2003 - 06:41:47 CST

Hello Layi,
both MM-GBSA and MM-PBSA are approximative methods, i.e. you run "proper"
explicit solvent simulation and then swithch to continuum solvent methods.
PB is more rigorous. For reviews, see

Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan
Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham III TE
(2000) Acc. Chem. Res. 33, 889-897

Massova I, Kollman PA, 2000:Combined molecular mechanical and continuum
solvent approach (MM-PBSA/GBSA) to predict ligand binding PERSPECTIVES IN
DRUG DISCOVERY AND DESIGN
18: 113-135

Hope this helps,

Martin

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----
Martin Lepsik, PhD student            Phone:  +420/2/20183-540, Fax:
+420/2/20183-292
Dept. of Theor Chem & Center for Complex molecular Systems and Biomolecules
Institute of Organic Chemistry and Biochemistry (IOCB)
Flemingovo nam 2,
Czech Academy of Sciences,
166 10, Prague 6,
Czech Rep.
URL: www.uochb.cas.cz/~teochem
----- Original Message -----
From: "Layi Adekoya" <adekoya_at_fagmed.uit.no>
To: "amber-heimdal.compchem.ucsf.edu" <amber_at_heimdal.compchem.ucsf.edu>
Sent: Wednesday, February 26, 2003 11:05 AM
Subject: mm_pbsa

> Hi,
> I have a question on MM_PBSA/GBSA.
> After MD simulation of the
> receptor, receptor complex and ligand in water.
> One removes the water and ions from the snapshots.
> The elctrostatic contribution is calculated either
> using PB or GB.
> my question is which will be more accurate
> GB or PB since we removed the solvent before running the script mmpbsa.in?
> Will it matter if one had water in the MD simulation but
> calculated elctrostatic contribution using
> GB alone for MM_GBSA?
>
> Thanks in advance.
>
> Layi