AMBER: partial charge

From: Li Ying <bj_0306.yahoo.com>
Date: Mon, 1 Dec 2003 09:31:56 -0800 (PST)

Dear Amber Users,
 
I try use Sander to minimize a 11-mer B-DNA in amber7. When I use XLeap to load the pdb file of this duplex, it shows total charge -20. But in output file of minimization, it says "Sum of charges from parm topology file = -9.9999999".
 
here is the minimization input file:
&cntrl
  ntb = 0,
  dielc = 4.0, cut = 9.0,
  scnb = 2.0, scee = 1.2,
 
  imin = 1,
  maxcyc = 1000, ncyc= 100,
&end
&ewald
  eedmeth = 5,
&end
 
 Why the total charge is not -20 in minimization? Thanks for your help.
 
Ying Li



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Received on Wed Jan 14 2004 - 15:53:03 PST
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