AMBER Archive (2004)

Subject: AMBER: PBCAL in mm-pbsa calculation

From: nlxc (nlxc2000_at_yahoo.com)
Date: Fri Jun 11 2004 - 12:26:21 CDT

Hi,
 
I am running mm-pbsa on a ligand-protein complex. Everything is fine except the PBCAL value(reaction field energy calculated by PB) for my ligand is always 0.00. Is that normal? Does anybody know what's the possible problem with my system. I ran MD simulation on complex for 500ps and used mm_pbsa.pl to extract 50 snapshots for complex, receptor and ligand without any water or countions.
 
Any suggestions are highly appreciated! Thanks in advance.
 
Nan
 

                
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