AMBER Archive (2004)

Subject: AMBER: PBCAL in MM/PBSA

From: nlxc (nlxc2000_at_yahoo.com)
Date: Fri Jun 25 2004 - 14:09:19 CDT

Hi,
 
I am using mm/pbsa to calculate bind energy of protein+ligand complex. Delphi is used to calculate PB value. My question is: Is there any recommendation or preference of which type of charge should be assiged to ligand (I use amber94 for protein) since I found a huge difference of PBCAL value of ligand(~10 kcal) comparing the results from gasteiger charge(for ligand) and AM1 charge(for ligand). Does anyone has the similiar experience? Your suggestion will be highly appreciated!
 
Thanks in advance.
 
Nan

                
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