Re: AMBER: Accuracy of PB solvation energy

From: Jiri Sponer <>
Date: Fri, 5 Sep 2003 19:46:04 +0200 (MEST)

> Dear Amber Users:
> Do you know how accurate the PB solvation energy
> (calculated by DelPhi) in MM-PBSA module usually is?
> The accuracy refers to comparison with experimental
> solvation energy, not to the deviation from the
> snapshots.
> Thanks,
> Qing Zhang

It very much depends on the system you wish to evaluate.

You may see for example
Molecular dynamics simulations and thermodynamics analysis of DNA-drug complexes.
Minor groove binding between 4 ',6-diamidino-2-phenylindole and DNA duplexes in solution
Spackova N et al,.
J. Am. Chem. Soc.
125 (7): 1759-1769 FEB 19 2003

Hydration energies in water are in fact an exceptionally difficult task for all
kinds of continuum models, not only classical (PB, GB) but also
QM-based ones (PCM, COSMO, etc...).
The results are parameter-dependent.
See for example:
Solvation free energies of the nucleic acid bases
Miller JL, Kollman PA
J. Phys. Chem .
100 (20): 8587-8594 MAY 16 1996

Best wishes, Jiri

Jiri Sponer
Institute of Biophysics
Academy of Sciences of the Czech Republic
Kralovopolska 135
CZ-61265 Brno
Czech Republic
fax: 420 5412 12179
phone: 420 5415 17133
Senior Wellcome Trust International Research Fellow for Biomedical Research

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Received on Fri Sep 05 2003 - 18:53:01 PDT
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