[AMBER] help with antechamber

From: <tsurma.umich.edu>
Date: Fri, 29 Apr 2011 15:12:35 -0400

Hi,

I need to make a diatomic CN- (cyanide ion) using a four site model, with
partial charges on N (-1e at z=1.17Angstrom) C (0e at z=0.0A position) and
two partial charge sites at 0.22A (-1.31e) and -0.22A (1.31e).

So, I changed the mol2 file and ran antechamber and got this:


.<TRIPOS>MOLECULE
CYN
    4 1 1 0 0
SMALL
No Charge or Current Charge


.<TRIPOS>ATOM
      1 C1 0.0000 0.0000 0.0000 c1 1 CYN
0.000000
      2 N1 0.0000 0.0000 1.1770 n1 1 CYN
-1.000000
      3 X1 0.0000 0.0000 -0.2200 DU 1 MOL
-1.000000
      4 X2 0.0000 0.0000 0.2000 DU 1 MOL
-1.000000
.<TRIPOS>BOND
     1 1 2 3
.<TRIPOS>SUBSTRUCTURE
     1 CYN 1 TEMP 0 **** **** 0 ROOT


I was wondering if it is correct or I am doing something totally wrong?

Thanks
Surma Talapatra
Graduate Student
Geva Group
University of Michigan



_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 29 2011 - 12:30:04 PDT
Custom Search