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.
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 ?
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?
Huge thanks in advance!
Qiong
On Mon, Oct 24, 2011 at 6:21 AM, Jason Swails <jason.swails.gmail.com>wrote:
> On Sun, Oct 23, 2011 at 1:41 AM, Qiong Zhang <qiong.zhang.qzh.gmail.com
> >wrote:
>
> > Dear Ray,
> >
> > Thank you for your suggestion.
> >
> > I had confusions before on all the scripts for mmpbsa calculations, the
> > perl
> > script in the pbsa module in AMBER, and the python script in the
> > Ambertools.
> > Some parameters in these two scripts have different meanings, which
> caused
> > extra confusions.
>
>
> Do you have examples of these? We try to be as consistent as possible
> between the 2 versions to limit these confusions. It's true that some
> variables have different defaults (and MMPBSA.py does have more adjustable
> parameters accessible via the input file), but the common ones should have
> the same name with the same meaning.
>
> Thanks,
> Jason
>
> Now I think I would do as you suggested, try to use the
> > newest release of *Ambertools 1.5 *for my problems.
> >
> > Many thanks again!
> >
> > Qiong
> >
> >
> > On Sun, Oct 23, 2011 at 6:19 AM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
> >
> > > Dear Qiong,
> > >
> > > May I suggest you to use the Ambertool release for your calculation so
> > > you may have a better control of all the input parameters, i.e. by
> > > following the manual suggested values? The perl scripts (including its
> > > comments) haven't been updated for a while ...
> > >
> > > All the best,
> > > Ray
> > >
> > > On Sat, Oct 22, 2011 at 1:56 PM, Qiong Zhang <
> qiong.zhang.qzh.gmail.com>
> > > wrote:
> > > > Dear all,
> > > >
> > > > I am now trying to use the pbsa module in AMBER11 to calculate the
> > > binding
> > > > free energy between a protein and a ligand.
> > > >
> > > > I have a question on the choice of the values for SURFTEN/SURFOFF.
> > > >
> > > > I read the AMBER manual on mm_pbsa and tried the test example. The
> > > following
> > > > are the descriptions for the two parameters both in the manual and in
> > the
> > > > input file for mm_pbsa calculations in the test example.
> > > >
> > > > # SURFTEN/SURFOFF - Values used to compute the nonpolar
> > > > # solvation free energy Gnp acccording to INP.
> > > > # If INP = 1 and RADIOPT = 0 (default, see above),
> > > > # 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.
> > > > # Otherwise, please
> > > > # set these to the following: SURFTEN: 0.04356; OFFSET:
> > -1.008
> > > >
> > > > It states clearly that 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.
> > > >
> > > > So I set INP = 2 and RADIOPT = 1, and commented the two lines for
> both
> > > > SURFTEN and SURFOFF. From the output file I found SURFTEN=1.0000 and
> > > > SURFOFF=0.000.
> > > >
> > > > However, in the test example (03_MMPBSA_Binding), when INP = 2 and
> > > RADIOPT =
> > > > 1, SURFTEN and OFFSET are set to be 0.04356 and -1.008, respectively.
> > > >
> > > > My question is when INP = 2 and RADIOPT = 1, what are exact values
> for
> > > > SURFTEN and SURFOFF please？
> > > >
> > > > Any suggestions and help would be greatly appreciated!
> > > >
> > > > Many thanks!
> > > >
> > > > Qiong Zhang
> > > >
> > > > Department of Theoretical Chemistry & Biology
> > > > School of Biotechnology
> > > > Royal Institute of Technology
> > > > Roslagstullsbacken 15
> > > > SE-10691 Stockholm, Sweden
> > > > _______________________________________________
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> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
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> > >
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> >
>
>
>
> --
> 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 - 13:00:03 PDT
