Dear amber users,
I am using antechamber to prepare my ligands.
One rather complex ligand contains a pyridine moiety.
After calculation of the partial charges (amber8 antechamber with the
AM1BCC method and divcon) I noticed a very small negative charge of the
nitrogen (-0.131).
I repeated the calculation for the pyridine molecule. The nitrogen
charge was calculated as -0.1385.
The same input structure used with an older version of antechamber and
mopac gave -0.6645 !
I noticed that the actual results obtained with mopac and divcon are
highly similar. The bcc correction does not seem to work with the new
antechamber version, at least in this case: the charges in the two files
ANTECHAMBER_AM1BCC.AC and ANTECHAMBER_AM1BCC_PRE.AC are identical.
Below you can see my command lines invoking antechamber and the two
resulting pyridine mol2 files.
Can somebody give me a hint on how to explain this?
Thanks very much,
Oliver
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Here are the mol2 files that came out of the two calculations for pyridine:
--- Results obtained with amber8 antechamber:
(antechamber -fi mol2 -fo mol2 -i pyridine.mol2 -o pyr_bcc_divcon.mol2
-j 5 -nc 0 -c bcc -s 2)
.<TRIPOS>MOLECULE
PYR
11 11 1 0 0
SMALL
bcc
.<TRIPOS>ATOM
1 C 1.2300 0.7100 0.0000 c2 1 PYR -0.1814
2 H 2.1630 1.2480 0.0000 ha 1 PYR 0.1427
3 C1 0.0000 1.4200 0.0000 c2 1 PYR -0.0932
4 H1 0.0000 2.4970 0.0000 ha 1 PYR 0.1374
5 C2 -1.2300 0.7100 0.0000 c2 1 PYR -0.1814
6 H2 -2.1630 1.2480 0.0000 ha 1 PYR 0.1427
7 C3 -1.2300 -0.7100 0.0000 c2 1 PYR -0.0726
8 H3 -2.1630 -1.2480 0.0000 ha 1 PYR 0.1584
9 N -0.0000 -1.4200 0.0000 n2 1 PYR -0.1385
10 C4 1.2300 -0.7100 0.0000 c2 1 PYR -0.0725
11 H4 2.1630 -1.2480 0.0000 ha 1 PYR 0.1584
.<TRIPOS>BOND
1 1 2 1
2 1 3 ar
3 1 10 ar
4 3 4 1
5 3 5 ar
6 5 6 1
7 5 7 ar
8 7 8 1
9 7 9 ar
10 9 10 ar
11 10 11 1
.<TRIPOS>SUBSTRUCTURE
1 PYR 1 TEMP 0 **** **** 0 ROOT
--- Results obtained with amber7 antechamber and mopac:
(antechamber -fi mol2 -fo mol2 -i pyridine.mol2 -o pyr_bcc_mopac.mol2 -j
5 -nc 0 -c bcc -s 2)
.<TRIPOS>MOLECULE
PYR
11 11 1 0 0
SMALL
GASTEIGER
.<TRIPOS>ATOM
1 C 1.2300 0.7100 0.0000 C 1 PYR
-0.2466
2 H 2.1630 1.2480 0.0000 H 1 PYR
0.1431
3 C 0.0000 1.4200 0.0000 C 1 PYR
-0.0934
4 H 0.0000 2.4970 0.0000 H 1 PYR
0.1375
5 C -1.2300 0.7100 0.0000 C 1 PYR
-0.2472
6 H -2.1630 1.2480 0.0000 H 1 PYR
0.1419
7 C -1.2300 -0.7100 0.0000 C 1 PYR
0.3933
8 H -2.1630 -1.2480 0.0000 H 1 PYR
0.0221
9 N -0.0000 -1.4200 0.0000 N 1 PYR
-0.6645
10 C 1.2300 -0.7100 0.0000 C 1 PYR
0.3928
11 H 2.1630 -1.2480 0.0000 H 1 PYR
0.0211
.<TRIPOS>BOND
1 1 2 1
2 1 3 ar
3 1 10 ar
4 3 4 1
5 3 5 ar
6 5 6 1
7 5 7 ar
8 7 8 1
9 7 9 ar
10 9 10 ar
11 10 11 1
.<TRIPOS>SUBSTRUCTURE
1 PYR 1 TEMP 0 **** **** 0 ROOT
--
_______________________________________________________________
Oliver Hucke, Dr.
Health Sciences Building - K418C
University of Washington 1959 NE Pacific St.
Dept. of Biochemistry phone: (206) 685 7046
Box 357742 fax : (206) 685 7002
Seattle, WA 98195-7742 email: ohucke.u.washington.edu
_______________________________________________________________
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Received on Fri Apr 23 2004 - 23:53:00 PDT
