AMBER Archive (2006)

Subject: AMBER: Ti calculations in dmso solvent

From: Vitor Manuel Sousa F?x (
Date: Mon Feb 20 2006 - 11:55:32 CST

Dear Amber users

We are interested to calculate the binding association
constant between a macrocyclic receptor and a carboxylate
anion with charges +5 and -2 respectively. The
experimental data were obtained in dmso solution and I
want to estimate the value of the constant in this medium
using the thermodynamic integration methods. The best way
to do that it is carry out two independent simulations as
described at amber home page for the transformation
toluene -> nothing in water. For the dimethyl sulfoxide
we are using the flexible model reported by kollman in J.
Phys. Chem 102,8070, 1998 and provided with amber.
 Unfortunately the values of the calculated constants are
largely overestimated when compared with experimental
ones. We would like to know if there is a more
appropriated DMSO solvent model for free energy
calculations?. .. The charges for anion and receptor were
calculated separately using the resp methodology. However
other charge models such as am1-bbc, other starting input
geometries in Gaussian were used. The resp charges were
also calculated for receptor and anion together but the
result was worsted then that obtained with charges
calculated independently.

Thank you very much in advance for your help


Vitor Felix
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