[Dock-fans] Error messages when docking specific molecules within ZINC-derived library

John J. Irwin jji at cgl.ucsf.edu
Fri Jul 20 16:37:15 PDT 2007


Hi Mike

If you are using DOCK 4, are you adding the "substructure" record to the
end of each mol2 entry as required?
Two methods are referenced on the ZINC home page:
http://blaster.docking.org/zinc/fix_substructure.py
http://blaster.docking.org/zinc/zinc_convert.csh.txt

If you are doing this already, please let me know and we will go on to
the next step.

Good luck!

John



Silberstein, Michael wrote:
> Hi,
>  
> I am a novice at docking larger libraries, and so, the following inquiry represents some of my current difficulties in docking (using DOCK 4.0.1) a ZINC-database derived mini-library.
>  
> I have attempted to dock a library of ~3000 compounds to various zinc-metalloproteases.  Even though 3000 separate molecules were included (in one large .mol2 file), only ~ 600 of them were able to provide docking results.  The remaining 2400 compounds gave the following error:
>  
> WARNING read_mol2: Error reading ATOM record for ZINC00001648 in ./xyz.mol2.
> WARNING read_mol2: Error reading ATOM record for ZINC00001825 in ./xyz.mol2.
> WARNING read_mol2: Improper BOND origin/target for ZINC00001932 in ./xyz.mol2.
> WARNING read_mol2: Error reading ATOM record for ZINC00002585 in ./xyz.mol2.
> WARNING read_mol2: Error reading ATOM record for ZINC00002588 in ./xyz.mol2.
> WARNING read_mol2: Error reading ATOM record for ZINC00002819 in ./xyz.mol2.
> WARNING read_mol2: Improper BOND origin/target for ZINC00003421 in ./xyz.mol2.
>  
> and so on...
>  
> Can anyone explain to me what might be wrong with the format of these individual .mol2 files such that either the ATOMs or BONDs cannot be read-in properly in order to have these molecules docked??
>  
> Since this analysis has been already performed using DOCK 4.0, it would be really good if I would not have to potentially repeat this using a newer version of DOCK.  So it would be preferable if any suggestions/comments be regarding (specifically) DOCK 4.0 and why the program is having trouble reading in such a large percentage of ZINC database-derived .mol2 files.  Any suggestion would be very helpful at this point.  Thanks in advance.
>  
>  
> Sincerely,
> Mike Silberstein
>  
>  
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