AMBER Archive (2007)

Subject: AMBER: Use of Counter Ions in binding energy calculations

From: Jonathan Suever (jsuever_at_uab.edu)
Date: Thu Dec 20 2007 - 12:42:15 CST

Amber users,
I have performed a molecular dynamics simulation on a protein-protein
complex with a non-zero overall charge (-17). In order to simulate the
physiological environment, we solvated the protein in a water box along with
Na+ and Cl- ions at a concentration of 150 mM. In order to neutralize the
system, I added counter-ions to the box. Using snapshots from the
trajectory (the snapshots contain the two proteins with no ions or counter
ions), I calculated the binding energy using mm_pbsa.pl.

>From a lot of the literature, it seems as though the electrostatic energy
and electrostatic contribution to the solvation free energy should be
similar in magnitude. In our system, these values differ by a factor of 4
(the electrostatic being larger in magnitude). I feel that the
miscalculation has to do with the parameters which have been selected for
the PB calculations. Below are the parameters which I am utilizing:

PROC 2
REFE 0

INDI 2.0
EXDI 78.4
SCALE 0.5

LINIT 1000
PRBRAD 1.4

ISTRNG 150
RADIOPT 0
NPOPT 1
CAVITY_SURFTEN 0.0072
CAVITY_OFFSET 0.00

SURFTEN 0.0072
SURFOFF 0.00

It seems that the main parameters to tweak would be the dielectric constants
and the ionic strength. I have already experimented with changing the
dielectric values for both the solute and the solvent. The only case in
which I get the PBCAL to be similar to ELE is when I set ISTRNG to 0.00. I
had originally chosen 150 because of the molarity of the "physiological
water" used during the simulation. Also, the example script as well as the
manual stated that the units for ISTRNG are indeed mM, is this correct?

My question comes to this: Are the values that I am expecting realistic
(PBCAL = ELE)? Since I have not included any ions explicitly in my
coordinates for processing, do I need to set ISTRNG = 150 mM? Are the units
for ISTRNG indeed mM? What might be some other potential reasons why I am
receiving the energy calculations that I am?

Thank you very much.

-Jonathan Suever
Researcher
University of Alabama at Birmingham

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