On Mon, Oct 24, 2011 at 3:50 PM, Qiong Zhang <qiong.zhang.qzh.gmail.com>wrote:
> Hi Jason and Ray,
>
> Thank you for your kind reply!
>
> I think I had confusions about the parameters cavity_surften/cavity_offset
> (in the python script in Ambertools) and SURFTEN/SURFOFF (in the perl
> script
> in AMBER). Now I think they should be of the same meaning but slightly
> different names and different default values.
>
SURFTEN and SURFOFF are the surface tension and offset values for GB.
CAVITY_SURFTEN and CAVITY_OFFSET are the surface tension and offset values
for PB (I thought this was the case for mm_pbsa.pl as well).
>
> I am wondering why in the perl script, the default values for
> SURFTEN/SURFOFF (If INP = 1 and RADIOPT = 0) is SURFTEN: 0.00542; SURFOFF:
> 0.92, while in the python script, the default values for
> cavity_surften/cavity_offset is 0.00542 and -1.008? Why the offset values
> used to correct nonpolar free energy contribution are so different ?
>
I can't comment on the reasoning behind the default values in mm_pbsa.pl,
but the MMPBSA.py values were chosen because they were the default values in
pbsa (have they changed since then?).
>
> Another thing that I am not sure is the relationship of MMPBSA.py and PBSA
> in ambertools. On page 201 in the manual for Ambertools 1.5, the default
> values for cavity_surften/cavity_offset is 0.00542 and -1.008 since the
> total non-polar solvation free energy is modeled as a single term linearly
> proportional to the solvent accessible surface area (default: INP=1). On
> page 169 in this manual, the default values for
> cavity_surften/cavity_offset
> are different since they are default values when INP=2. As far as I
> understood, in MMPBSA, the PB equation is solved numerically by the PBSA
> program in Ambertools. My question is that is it possible to use all the
> parameters in PBSA for MMPBSA calculations? I would like to use the
> optimized parameters as reported by Ray [J. Phys. Chem. B 2007, 111,
> 12263-12274] for the MMPBSA calculations. How could I do that please?
>
The manual outlines the input variables provided for MMPBSA.py, which is not
a full subset of the functionality implemented in pbsa. However, MMPBSA.py
adds flexibility via the -make-mdins and -use-mdins flags, which will create
the mdin files (first flag) to allow you to modify them, and then use the
modified mdin files (second flag) with your new values.
Note that because MMPBSA.py uses PBSA routines through its NAB interface,
those options provided in that interface are the only ones accessible to
MMPBSA.py (unless you specify use_sander, then you'll have sander's options
at your disposal).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Oct 24 2011 - 13:30:03 PDT
