AMBER Archive (2004)

Subject: AMBER: Antechamber: problems with bcc correction

From: Oliver Hucke (ohucke_at_u.washington.edu)
Date: Fri Apr 23 2004 - 17:08:47 CDT

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

--------------------------------------------------------------------------

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_at_u.washington.edu
_______________________________________________________________

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu