Hi,
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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Received on Tue Jun 08 2004 - 08:53:00 PDT
