ADL: Atom types.

Oleg Trott trott at scripps.edu
Wed Jun 17 10:18:35 PDT 2009


On Tue, Jun 16, 2009 at 2:51 AM, Vitor Hugo Teixeira<vhteixeira at ualg.pt> wrote:
> Hi!
>
> I tried vina in some previous complexes I was working on, and I found that
> vina, contrary to autodock 4 has no support for atom types like Fe or Zn.

What makes you say that? They should be accepted. Many a Fe and Zn
were in the training set even.

I suspect that you misspelled them in your PDBQT file's last column as
FE and ZN, and are getting an error that these are unknown atom types.
This is because atom types are case-sensitive, to distinguish Na
(sodium) and NA (nitrogen H-bond acceptor).

Best of luck,
Oleg
-- 
Oleg Trott, Ph.D. (Columbia University)

http://olegtrott.com


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