ADL: Problem with AutoDock Vina Modeling

Gustavo Seabra gustavo.seabra at gmail.com
Tue Aug 11 13:49:55 PDT 2020


I'm sorry, but that is a bit beyond my abilities at the moment. I suggest
you try the lists archives first, as people have parameterized other atoms
before. I just don't have this experience to guide you there, sorry!
--
Gustavo Seabra.


On Tue, Aug 11, 2020 at 4:31 PM Tram B. Danh <tbdanh at uci.edu> wrote:

> Hi Gustavo,
>
> Thank you for your reply. I've been looking at AutoDock but was not able to
> derive the parameter for At. Can you show me how to do so?
>
> Thank you,
> Tram Danh
>
> On Tue, Aug 11, 2020 at 12:15 PM Gustavo Seabra <gustavo.seabra at gmail.com>
> wrote:
>
> > That happens because there are no parameters for At i the database. Take
> a
> > look at:
> >
> >
> http://autodock.scripps.edu/faqs-help/faq/missing-atom-types-201cwhy-atom-type-x-is-not-recognized-201d
> >
> > You may have to derive the parameters yourself if you really need them.
> > --
> > Gustavo Seabra.
> >
> >
> > On Tue, Aug 11, 2020 at 3:05 PM Tram B. Danh <tbdanh at uci.edu> wrote:
> >
> > > To whom it may concern,
> > >
> > > My name is Tram Danh, an undergraduate researcher under the Radiology
> > > Department at the University of California, Irvine. I have encountered
> > > problems as I tried to run AutoDock Vina for a structure with At
> > > (Astatine). The system said that the atom At was not assigned or
> > > recognized. The structure was successfully obtained via ChemDraw, so I
> > > couldn't figure out why atom At caused the error. Could you please help
> > me
> > > solve this problem?
> > >
> > > Thank you for your time! I hope to hear back from you soon!
> > >
> > > Sincerely,
> > > Tram Danh
> > > B.S. Pharmaceutical Sciences | 2021
> > > Student Researcher Radiology | Department
> > > University of California, Irvine
> > > tbdanh at uci.edu
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> >
> >
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>


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