Dear Jason,
Thanks very much for you detailed explanations. I will have a test on this
problem, and if I have problems, I will be here. Thanks!
Best Regards,
Qinghua
On Mon, Dec 12, 2011 at 10:21 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Mon, Dec 12, 2011 at 9:00 AM, Qinghua Liao <fantasticqhl.gmail.com
> >wrote:
>
> > Dear amber users,
> >
> > In python pbsa, the default option of* inp* is 1 (it is not clear
> whether 2
> > is available in the manual), and the default *cavity_surften* and *
> > cavity_offset* are 0.00542 and -1.008 respectively. However, in the perl
> > version, the explanations from the manual are different:
> >
> > If INP = 1 and RADIOPT = 0 (default), use SURFTEN/SURFOFF parameters that
> > fit with the radii from the prmtop file, e.g., use SURFTEN:
> > 0.00542; SURFOFF: 0.92 for PARSE radii. If INP = 2 and RADIOPT = 1, these
> > two lines can be removed, i.e., use the default values set in pbsa for
> this
> > nonpolar solvation model. Otherwise, set these to the following: SURFTEN:
> > 0.04356; OFFSET: -1.008
> >
> >
> > So why is the default value of cavity_offset -1.008, but not 0.92 in the
> > python version? Is inp of 2 available in python version? Another
> question,
> > will the results be the same calculated by python and perl versions using
> > the same parameters? Does someone test it?
> >
>
> The defaults in the Python version were adjusted to match the defaults used
> in PBSA itself, rather than the defaults used in mm_pbsa.pl. This is the
> reason for the difference. Furthermore, MMPBSA.py exposes all of the
> variables from PBSA that are present in the NAB interface (see the NAB
> documentation regarding inp) or sander (see the Amber 11 source code). If
> INP==2 is available there, it should be available in MMPBSA.py, too.
>
> When we first wrote the Python version, we carefully tested the results
> between the Python and Perl versions to see that they matched to reasonable
> certainty. However, a couple things will always cause differences. The
> use of (very) limited precision in ASCII trajectory/coordinate files makes
> the results change with molecule orientation (since internal coordinates
> change when limited-precision cartesians are arbitrarily rotated and/or
> translated).
>
> Within the tolerances of these effects, the two versions give the same
> answers as long as you provide exactly the same parameters.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Tue Dec 13 2011 - 00:00:03 PST
