AMBER Archive (2002)

Subject: Re: betaP,SURFOFF inconsistency

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Sun Sep 22 2002 - 15:20:03 CDT

Dear Martin,

you are right - the "0.092" value slipped into a (early) amber7 mm_pbsa
version by copy-and-paste. There is no "factor 10" multiplication within
mm_pbsa, so Barry Honig's et al. "0.92 kcal/mol" should be used as
SURFOFF parameter together with the PARSE radii provided in the Example
directory. Since it is the offset in a linear equation, the non-polar
contribution to solvation energy is too small by 0.828 kcal/mol for a
"stability calculation", leading to binding free energies which are too
large (i.e. underestimate binding) by the same amount.

Thank you for reporting this!

Holger

>>>>>

Dear AMBER community,
in MM-PBSA module, I have found an inconsistency in the value of betaP
(SURFOFF)parameter. In the example scripts of amber6 and amber7 as well
as in some papers using
mm_pbsa I've seen the value of 0.092, whereas in the papers from Barry
Honig's lab, there's
the value of 0.92kcal/mol.

Please can you tell me which one is the correct one? Or I imagine both
could be provided in the script the value is multiplied by 10 (could
Holger comment on this?)

Did someone try out to see the differences in results using these two
values?

looking forward to your replies.

sincerely,

     Martin
------------------------------------------------------------------------------------------------------------------------------------------------------------
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

<<<<< 

-- 
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
email: gohlke_at_scripps.edu
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