AMBER Archive (2004)

Subject: AMBER: Partial Charge on ligand for MD & MM/PBSA

From: Nan Lin (
Date: Mon Jun 07 2004 - 21:11:25 CDT

I am running a MD for a complex of protein + ligand with WAT. I follows the procedures of a paper and hope to get the similar results of binding energy calculation from MM/PBSA as the data shown. Although the results of vdw + SA is fairly similiar, the ELEC + PB is far different. I am not sure if the partial charge of ligand or protein cause this big difference because I use Gasteiger charges, but the paper used AM1-BCC or PM3 charges. So my question is: do those different parital charges methods cause such a difference in the calculation of ELEC and PB or something else may be wrong in my system?
Your help is highly appreciated!

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