Hi All,
I would like to see the effect of internal dielectric constant in the
binding free energy calculated by MMPBSA.py. However, putting indi=2, I can
only get the polar solvation energy scaled 67.8997/137.9406=0.492. But the
direct electrostatic contribution stays not scaled. I think in order to get
the direct electrostatic energy scaled, dielectric constant needs to be set
for sander. However, I have not found the related variable for MMPBSA.py
input. Although I can manually divide the direct electrostatic energy by
the internal dielectic constant, it would be better if it could be done
directly with the script.
Thanks!
Qiong
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jul 24 2012 - 18:30:04 PDT
