Re: [AMBER] results calculated by and

From: Jason Swails <>
Date: Thu, 1 Jul 2010 10:55:50 -0400

It could simply be what you chose to print out in each case. For,
only terms that you print to the output file according to the "verbose"
variable are added to the total and gas/solvation terms. It would help if
you posted your two output files so we can take a look at them. There's a
chance that one of the two scripts may be adding in the bonded terms (such
as 1-4 interactions, bond, angle, and dihedral). Ultimately, though, none
of this affects the differences, since all of those terms cancel out in the
end, anyway. That's why the delta G was almost the same. Also take note of
whether or not you're using molsurf to calculated the nonpolar solvation
free energy term with does not have an option to use
molsurf, and simply relies on the LCPO method built into sander. This will
cause some numerical differences in this term (ESURF or ENPOLAR or ECAVITY
or something of the like).

Hope this helps,

2010/7/1 <>

> Dear all:
> I calculated the binding free energy by using and
> methods respectively,the values of delataG by the two approaches
> were almost the same, however, the values of the different energy terms have
> a considerable differences.why?
> the version of amber i use is amber10.
> thank you!
> -linda
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Thu Jul 01 2010 - 08:00:07 PDT
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