[Dock-fans] skipped compounds

Scott Brozell sbrozell at scripps.edu
Thu Mar 29 09:19:28 PST 2007


Hi,

Thanks for the report.  I am planning to investigate this.

Scott

On Thu, 22 Mar 2007, Philip Crawford wrote:

> Scott,
> I haven't run Dock 6.1 in MPI mode but Dock 6, when running in MPI mode,
> only lists the compounds which get valid scores.
>
> I was trying to run on a small binding site (benzoate was the inhibitor in
> the known structure) and I found in non-MPI mode Dock6 was listing lots of
> molecules with an error, suggesting the grid may not be large enough. This
> doesn't happen when running a library through in MPI mode.
>
> I can't recall but I think it reported the correct number of molecules
> processed when running in MPI mode. Just didn't fill the Dock.out file with
> messages about molecules which don't fit.
>
> -----Original Message-----
> From: dock-fans-bounces at docking.org [mailto:dock-fans-bounces at docking.org]
> On Behalf Of Scott Brozell
> Sent: Thursday, 22 March 2007 5:12 PM
> To: Yuliet Mazola Reyes
> Cc: dock-fans at docking.org
> Subject: Re: [Dock-fans] skipped compounds
>
> On Wed, 21 Mar 2007, Yuliet Mazola Reyes wrote:
>
> > 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.
>
> My comments are based on the a brief look at the source code, but there are
> a lot of paths through the code.  I am using this input
> install/test/bump_filter/bump2.dockin
> to verify my statements.
>
> Every molecule in the ligand_atom_file should have its title emitted like
> this, e.g.:
>
> -----------------------------------
> Molecule: ZINC00157467
>
> And every molecule in the ligand_atom_file should be tallied in this line at
> the tail of the dock output, e.g.:
>
> 12 Molecules Processed
>
> Thus, you should be able to account for every molecule in the
> ligand_atom_file.
>
> > 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?
>
> What is the "compounds skipped line in the info file" ?
>
> It appears that there is no output what so ever when something is skipped
> via the bump filter.
> If docking of a molecule is not successful then either this:
>
> ERROR:  Could not find valid anchor orientation.
>
> or this:
>
> ERROR:  Could not complete growth.
>
> will be emitted.
>
>
> > 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.
>
> If those lines are present then they are read and saved.
> If those lines are not present then they are not read.
> Thus DOCK is robust with respect to those optional data lines;
> http://www.tripos.com/mol2/mol2_format25.html#1184
>
> Scott
>
> > 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


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