ADL: Help in covalent docking using autodock vina

Oleg Trott trott at
Mon Jan 6 17:47:07 PST 2014


There are two ways in which people do "covalent docking" with
AutoDock: using pseudoatoms to keep some anchor atom next to a
predetermined spot, or by treating the ligand like a side chain,
covalently attached to the protein. With Vina, you should probably use
the second method, as Vina doesn't take pseudoatoms. All atom types in
the ligand should be recognizable by Vina, of course.

On Mon, Dec 23, 2013 at 7:00 AM, tusharranjanmoharana
<tusharranjan at> wrote:
> Hi,
> When I tried to perform a covalent docking using ADT and autodock vina I got
> the following message
> Unknown atom type Z in ligand.
> I will be grateful if someone can suggest anything.
> Thanks
> Tushar
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Oleg Trott, Ph.D. (Columbia University)

Staff Scientist in the Olson Lab
The Scripps Research Institute

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