ADL: "Broken" Ligand

Daan van Aalten vdava at davapc1.bioch.dundee.ac.uk
Thu Sep 9 12:59:51 PDT 2004


Hi Catherine

Perhaps your ligand topology is screwed - you could try the PRODRG server
which writes autodock topologies for small molecules.
(http://davapc1.bioch.dundee.ac.uk/prodrg)

cheers

Daan


On Thu, 9 Sep 2004, 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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>



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