AMBER Archive (2003)

Subject: AMBER: partial charge

From: Li Ying (bj_0306_at_yahoo.com)
Date: Mon Dec 01 2003 - 11:31:56 CST

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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