[AMBER] parameters in mm/pbsa calculations using python and perl versions

From: Qinghua Liao <fantasticqhl.gmail.com>
Date: Mon, 12 Dec 2011 15:00:14 +0100

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?

Best Regards,

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Received on Mon Dec 12 2011 - 06:30:03 PST
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