AMBER: Internal dielectric and MMPBSA

From: Ileana Stoica <>
Date: Tue, 12 Jun 2007 12:32:17 +0100

I am looking at the effect of the internal dielectric constant
on MMPBSA ligand binding energies.

Normally, both the MM Coulomb energies and the PB polar solvation
component should change with the internal dielectric, labelled
DIELC and INDI respectively.

Indeed, if I set DIELC=INDI=1, I get:

# -----------------------
# =======================
ELE -32.90 9.16
PBCAL 67.53 7.53

and when I set DIELC=INDI=10, I get as expected:

ELE -3.29 0.92
PBCAL 0.56 0.06

However, if in addition to MM=1 and PB=1, I also happen to have
GB=1 in the Mmpbsa input, the results for DIELC=INDI=10 look like:

ELE -32.90 9.16
PBCAL 0.56 0.06

The Coulomb energies are no longer scaled and consequently the new PBTOT is
So, it appears that to get the expected scaling of electrostatics,
we NEED to have in the input file:

PB=1 AND GB=0.

Is this true or am I missing something? It certainly can lead to confusing

Thank you,


Ileana Stoica
University College London

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Received on Wed Jun 13 2007 - 06:07:30 PDT
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