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
-1.310000
4 X2 0.0000 0.0000 0.2000 DU 1 MOL
1.310000
.<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
PS: the last mail ha a mistake so I am sending it again.
-------- Original Message --------
Subject: help with antechamber
Date: Fri, 29 Apr 2011 15:12:35 -0400
From: <tsurma.umich.edu>
To: amber.ambermd.org
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
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Received on Fri Apr 29 2011 - 13:00:03 PDT
