On Mon, Oct 24, 2011 at 10:20 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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 think this is right for MMPBSA.py. But for mm_pbsa.pl, as I saw in manual
for amber11 page 242, SURFTEN and SURFOFF are also the surface tension and
offset values for PB.
>
> >
> > 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).
>
Now I am more clear about the implementation. This really helps! Thank you a
lot!
Qiong
>
> HTH,
> Jason
>
> --
> 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Oct 24 2011 - 14:30:03 PDT
