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
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Oct 23 2011 - 21:30:03 PDT
