[Dock-fans] skipped compounds

Yuliet Mazola Reyes yuliet.mazola at cigb.edu.cu
Wed Mar 21 04:33:15 PST 2007


Hello:

I am docking a database of chemical compounds, and I noticed that some
compounds were not docked into the receptor and they are not reported in
the WARNING read_mol2 lines of the dock output file, which seems that
their MOL2 files shouldn't have problems to be read by Dock. I am using
the bump filter option to avoid bad orientations which overlap with the
receptor and do not score them.
I would like to know if compounds that do not pass the bump filter are
counted or reported in "compounds skipped" line in the info file or they
will be just excluded by Dock, and are not reported in the info file and
either in a WARNING line in the output dock file?
Is there an option to allow the user to know which compounds are
rejected by bump filter?

I also want to know if lines 13 and 14 which are blank in the original
SYBYL MOL2 file, separating  <TRIPOS>MOLECULE record from <TRIPOS>ATOM
record (see example of MOL2 file bellow), are ignored by Dock or they
should be kept blank to allow the reading of MOL2 file by Dock program.

SYBYL MOL2 EXAMPLE

1      #         Name: benzene
2      #         Creating user name: tom
3      #         Creation time: Wed Dec 28 00:18:30 1988
4
5      #         Modifying user name: tom
6      #         Modification time: Wed Dec 28 00:18:30 1988
7
8      @<TRIPOS>MOLECULE
9      benzene
10     12 12 1 0         0
11     SMALL
12     NO_CHARGES
13
14
15     @<TRIPOS>ATOM
16     1       C1      1.207   2.091   0.000  C.ar    1      BENZENE 0.000
17     2       C2      2.414   1.394   0.000  C.ar    1      BENZENE 0.000
18     3       C3      2.414   0.000   0.000  C.ar    1      BENZENE 0.000
19     4       C4      1.207   -0.697 0.000   C.ar    1      BENZENE 0.000
20     5       C5      0.000   0.000   0.000  C.ar    1      BENZENE 0.000
21     6       C6      0.000   1.394   0.000  C.ar    1      BENZENE 0.000
22     7       H1      1.207   3.175   0.000  H       1      BENZENE 0.000
23     8       H2      3.353   1.936   0.000  H       1      BENZENE 0.000
24     9       H3      3.353   -0.542 0.000   H       1      BENZENE 0.000
25     10      H4      1.207   -1.781 0.000   H       1      BENZENE 0.000
26     11      H5      -0.939 -0.542 0.000    H       1      BENZENE 0.000
27     12      H6      -0.939 1.936    0.000  H       1      BENZENE 0.000
28     @<TRIPOS>BOND
29     1       1       2       ar
30     2       1       6       ar
31     3       2       3       ar
32     4       3       4       ar
33     5       4       5       ar
34     6       5       6       ar
35     7       1       7       1
36     8       2       8       1
37     9       3       9       1
38     10      4       10      1
39     11      5       11      1
40     12      6       12      1
41 @<TRIPOS>SUBSTRUCTURE
42     1       BENZENE 1       PERM    0      ****    ****   0       ROOT

Thanking in advance,
Yuliet




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