> 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
e-mail: sponer.ncbr.chemi.muni.cz
fax: 420 5412 12179
phone: 420 5415 17133
http://www.ibp.cz/labs/LSDNA/
Senior Wellcome Trust International Research Fellow for Biomedical Research
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Received on Fri Sep 05 2003 - 18:53:01 PDT
