As far as I can remember, I do not recall any changes in default PB
parameters within MMPBSA.py. However, the defaults in the pbsa routines
called by sander may have changed between versions. You should be able to
check the mdout files produced by MMPBSA.py. Prior to the energy
calculations, the mdout file should contain a list of all the input
variables used for the sander calculation. If you compare the output files
from sander in Amber 10 and Amber 11, any differences should be the cause
of any discrepancies you see in the results. And since EPB is the only
value that is different, you should only have to compare the PB input
variables listed in those files.
I hope that helps.
-Bill
On Wed, Jun 6, 2012 at 11:18 AM, Damodaran, Komath <
Komath.Damodaran.elan.com> wrote:
> Hi,
>
> I have a puzzle with MMPBSA calculations using Sander in Amber10 and
> Amber11 versions.
>
>
>
> I am running MMPBSA calculations on a moderate size protein:ligand
> complex (about 300AAs).
>
>
>
> When I use the same topology, trajectory and inpcrd files along with
> the same mdinp options, the EPB value is lower in Amber 10 by about
> 12kcal/mol. All other numbers (vdw, Coulomb term, cavity term) match
> between Amber 10 and Amber 11.
>
>
>
> I am wondering if any of the default parameters have changed between
> versions 10 and 11.
>
>
>
> Here are the input options that I use.
>
>
>
> &cntrl
>
> nsnb=99999, ntb=0, cut=999.000000, imin=5,igb=10,
>
> /
>
> &pb
>
> sprob=1.400000, maxitn=1000, fillratio=4.000000
>
> radiopt=0, npopt=1, dbfopt=1, cavity_surften=0.005240,
>
> /
>
> END
>
>
>
> Thanks!
>
> Dam
>
>
>
>
>
>
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--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Wed Jun 06 2012 - 09:00:03 PDT
