ADL: Using ADT to Prepare Molecules for AutoDock

Matthew Stuible matthew.stuible at
Sat Apr 15 09:42:07 PDT 2006


I'm also interested in this question. It has been suggested previously 
to use the ProDRG server to prepare energy-minimized ligand structures 
with partial charges. However, I am currently trying to dock a compound 
containing an azolidinedione ring, and the partial charges on the 
heteroatoms generated by ProDRG seem unreasonably high. The partial 
charge estimates for this ring generated by ADT are more reasonable. 
However, the compound also contains a nitro group, and ADT can't handle 
nitro groups properly (they end up with a net charge of ~ -1). Finally, 
these two software packages also generate dramatically different charge 
estimates for halogens.

Is there any free software that could do a better job? I work in a 
molecular biology lab and I couldn't justify purchasing software like SYBYL.



Jean Spencer wrote:
> Hi,
> I have been using ADT to prepare my molecules for AutoDock.  However, in
> the literature, everyone seems to mention other software (for example,
> SYBYL) that was used to prepare the molecules for docking.  The AutoDock
> user's guide also suggests other software for this step.
> Since I am unable to buy any other software at the moment, what are the
> issues concerning molecules prepared by ADT?
> Thank you for your help.
> Jean
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