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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Received on Wed Jun 06 2012 - 08:30:03 PDT
