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

Silberstein, Michael mikesilb at bnl.gov
Wed Jul 11 06:26:41 PDT 2007


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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