ADL: "Broken" Ligand

Carsten Detering detering at u.washington.edu
Thu Sep 9 16:18:32 PDT 2004


Hi Catherine,

I have had this problem before, which was in my case a problem (bug?) in 
autotors. Have you checked your input ligand.pdbq file? If it is also 
corrupted, it might help to name all your atoms by the types only (i.e. 
C2 -> C, NH2 -> N etc).

Hope this helps,

Carsten

Catherine Hayes wrote:

> Dear All
> 
> I have used AutoDock to dock a ligand into a protein, but the conformations 
> that AutoDock presents me with, are all "disjointed". In some cases the ligand 
> has been broken into two pieces, in others into three. I have docked other 
> ligands into this particular protein, and nothing like this has happened 
> before. Can anyone suggest what may be happening?
> Thanks
> Catherine.
> 
> Catherine Hayes BSc MSc
> Protein Crystallography Group
> National University of Ireland Galway
> 
> ________________________________________________
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