ADL: Best way to assign partial charges

Douglas Houston dhouston at staffmail.ed.ac.uk
Tue Apr 21 04:56:08 PDT 2009


It seems that the Gasteiger charges calculated by prepare_ligand4.py are
indeed different from the Gasteiger charges calculated by OpenBabel.

Most of them aren't that different, but some are significantly different.
For example, atom 5 in this molecule below is quite negatively charged using
one method, and slightly positively charged using the other. Since nitrogen
is more electronegative, it seems to me that it would draw electrons from
the carbons it's bonded to and would indeed have a small negative charge, so
it appears that, in this case, the OpenBabel method is more "correct"
(please correct me if I'm wrong).

Charges added by OpenBabel 2.2.1:

ROOT
ATOM      1  C   LIG d  11       0.000   0.000   0.000  0.00  0.00    -0.002
C 
ATOM      2  C   LIG d  11      -0.595  -1.258  -0.587  0.00  0.00    -0.034
A 
ATOM      3  C   LIG d  11       0.699  -1.260   2.083  0.00  0.00     0.065
C 
ATOM      4  C   LIG d  11       0.000   0.000   1.540  0.00  0.00     0.014
C 
ATOM      5  N   LIG d  11       2.106  -1.152   1.669  0.00  0.00    -0.295
N 
ATOM      6  C   LIG d  11      -0.599  -2.453   0.142  0.00  0.00    -0.042
A 
ATOM      7  C   LIG d  11      -0.007  -2.512   1.530  0.00  0.00     0.054
C 
ATOM      8  C   LIG d  11       1.476   0.000  -0.440  0.00  0.00     0.027
C 
ATOM      9  C   LIG d  11       2.245  -1.168   0.206  0.00  0.00     0.086
C 
ATOM     10  C   LIG d  11      -1.148  -1.220  -1.872  0.00  0.00     0.049
A 
ATOM     11  C   LIG d  11      -1.154  -3.611  -0.415  0.00  0.00     0.007
A 
ATOM     12  C   LIG d  11      -1.704  -2.378  -2.429  0.00  0.00     0.117
A 
ATOM     13  C   LIG d  11      -0.767   1.212  -0.522  0.00  0.00     0.016
C 
ATOM     14  C   LIG d  11      -1.707  -3.573  -1.701  0.00  0.00     0.045
A 
ATOM     15  C   LIG d  11      -1.433   0.067   2.061  0.00  0.00     0.010
C 
ENDROOT
BRANCH   5  16
ATOM     16  C   LIG d  11       2.873  -2.267   2.244  0.00  0.00     0.112
C 
BRANCH  16  17
ATOM     17  C   LIG d  11       3.946  -1.722   3.155  0.00  0.00    -0.013
C 
ATOM     18  C   LIG d  11       4.773  -2.562   3.793  0.00  0.00    -0.078
C 
ATOM     19  C   LIG d  11       5.847  -2.017   4.704  0.00  0.00     0.038
C 
ATOM     20  C   LIG d  11       4.631  -4.053   3.600  0.00  0.00     0.038
C 
ENDBRANCH  16  17
ENDBRANCH   5  16
BRANCH  12  21
ATOM     21  O   LIG d  11      -2.244  -2.341  -3.688  0.00  0.00    -0.507
OA
ATOM     22  H   LIG d  11      -2.242  -1.433  -4.241  0.00  0.00     0.292
HD
ENDBRANCH  12  21
TORSDOF 3

Charges added by prepare_ligand4.py:

ROOT
HETATM    1  C   LIG     1       0.000   0.000   0.000  1.00  0.00    -0.009
C 
HETATM    2  C   LIG     1      -0.595  -1.258  -0.587  1.00  0.00    -0.040
A 
HETATM    3  C   LIG     1       0.699  -1.260   2.083  1.00  0.00     0.232
C 
HETATM    4  C   LIG     1       0.000   0.000   1.540  1.00  0.00     0.028
C 
HETATM    5  N   LIG     1       2.106  -1.152   1.669  1.00  0.00     0.097
N 
HETATM    6  C   LIG     1      -0.599  -2.453   0.142  1.00  0.00    -0.049
A 
HETATM    7  C   LIG     1      -0.007  -2.512   1.530  1.00  0.00     0.075
C 
HETATM    8  C   LIG     1       1.476   0.000  -0.440  1.00  0.00     0.044
C 
HETATM    9  C   LIG     1       2.245  -1.168   0.206  1.00  0.00     0.274
C 
HETATM   10  C   LIG     1      -1.148  -1.220  -1.872  1.00  0.00     0.045
A 
HETATM   11  C   LIG     1      -1.154  -3.611  -0.415  1.00  0.00     0.010
A 
HETATM   12  C   LIG     1      -1.704  -2.378  -2.429  1.00  0.00     0.066
A 
HETATM   13  C   LIG     1      -0.767   1.212  -0.522  1.00  0.00     0.021
C 
HETATM   14  C   LIG     1      -1.707  -3.573  -1.701  1.00  0.00     0.037
A 
HETATM   15  C   LIG     1      -1.433   0.067   2.061  1.00  0.00     0.013
C 
ENDROOT
BRANCH   5  16
HETATM   16  C   LIG     1       2.873  -2.267   2.244  1.00  0.00     0.300
C 
BRANCH  16  17
HETATM   17  C   LIG     1       3.946  -1.722   3.155  1.00  0.00     0.005
C 
HETATM   18  C   LIG     1       4.773  -2.562   3.793  1.00  0.00    -0.090
C 
HETATM   19  C   LIG     1       5.847  -2.017   4.704  1.00  0.00     0.042
C 
HETATM   20  C   LIG     1       4.631  -4.053   3.600  1.00  0.00     0.042
C 
ENDBRANCH  16  17
ENDBRANCH   5  16
BRANCH  12  21
HETATM   21  O   LIG     1      -2.244  -2.341  -3.688  1.00  0.00    -0.361
OA
HETATM   22  H   LIG     1      -2.242  -1.433  -4.241  1.00  0.00     0.217
HD
ENDBRANCH  12  21
TORSDOF 3

I plan to re-dock a large number of molecules using the new charges and see
if they make a big difference to the rankings.
-- 
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