AMBER Archive (2006)

Subject: AMBER: optimatized structure is so much different from the original pdb structure

From: emilia wu (
Date: Thu Nov 16 2006 - 23:38:18 CST


I am doing some calculation about the binding between inhibitor and protein, and I use Gaussian to
get the charge parameters of inhibitor with resp fitting. after the optimization with HF/6-31G**, I got a
conformation which is so different from the origianl conformation from the protein data bank that
it turn over from one side to the other. I just want to know whether we can use this Gaussian log file
to get the prepi file for calculating the binding energy. does it matter to the later calculation?
thanks in advance!

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