On Tue, Jun 25, 2013 at 11:29 AM, Hannes Loeffler <
Hannes.Loeffler.stfc.ac.uk> wrote:
> On Tue, 25 Jun 2013 08:39:37 -0400
> Jason Swails <jason.swails.gmail.com> wrote:
>
> > On Tue, Jun 25, 2013 at 8:28 AM, Hannes Loeffler
> > <Hannes.Loeffler.stfc.ac.uk
> > > wrote:
> >
> > > Hi Jason,
> > >
> > > Force field is ff12SB. I now made sure that MMPBSA.py is the one
> > > from AmberTools 13 (from the comment on the top: "Last updated:
> > > 12/03/2012")
> > > - with the error message now appearing... I have %FLAG RADIUS_SET
> > > (mbondi) and %FLAG RADII set in the parmtop though.
> > >
> >
> > An easy way to tell if the version is 'correct':
> >
> > MMPBSA.py --version
> >
> > Even the Python programs have to be 'reinstalled' following an update
> > (in case you just ran update_amber or something without re-running
> > configure/make install).
> >
> >
>
> Ok, thanks. It's version 13.0. But how do I get the radii.
>
Which radii? At this point, it should just be using the values in the
prmtop file (you can get those values from ParmEd using the printDetails
command on the mask .%2C,3C,C8,CO).
Otherwise, I would compare the atom types from parm12, see where they're
used in ff99SB, and assign the same radii as would be assigned in ff99SB.
For instance, 2C is used as the CB atom type in amino12.lib. In
all_amino94.lib (the version used for ff99SB), that atom type is CT. So
however CT is assigned in PBSA, I would assign that same value to 2C. You
can use the same reasoning for the remaining atoms.
All the best,
Jason
P.S. A disclaimer: I don't work on PBSA and haven't looked into the
non-polar solvation methods in detail. The above approach seemed logical
to me, but take it as it is :)
--
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 Tue Jun 25 2013 - 09:00:03 PDT
