ADL: Autotors and large sets of ligands

Carsten Detering detering at u.washington.edu
Thu Sep 23 09:16:42 PDT 2004


Dear Vincenzo,

I have done it with a small database and the foreach loop. You need to 
be careful though, because sometimes the value TDOF at the end of the 
pdbq file does not match the actual number of torsions (hydrogen rotors 
dont count as a torsion for the torsdof value in the dpf file). You also 
have to find a way of parsing the TDOF value of the pdbq file into the 
dpf file (torsdof). A little script running sed helped me here.
Another thing is that autotors sometimes doesnt get the connectivity of 
some ligands. I made the experience that naming the atoms only by their 
element name (i.e. NH2 -> N; C2 -> C) does the trick.

Hope this helps.

Carsten

vincenzo.tschinke at speedel.com wrote:
> I am preparing large sets of ligands for docking. It looks like using 
> autotors with the 
> 
> -r
> 
> flag can work in a fully automated fashion, generating all the needed 
> "pdbq" files without 
> user intervention. Is there any caveat with such procedure? Any (better) 
> alternative?
> 
> Thanks
> 
> 
> 
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