ADL: Problem with AutoDock Vina Modeling

Tram B. Danh tbdanh at uci.edu
Wed Aug 12 16:40:46 PDT 2020


Hello,

I tried to derive the parameter for At in AutoDock but it didn't work. Is
there a way to add a new atom to AutoDock Vina instead? Or changes made in
AutoDock would be automatically updated in AutoDock?

Thank you,
Tram Danh


On Tue, Aug 11, 2020 at 7:03 PM Van Dam, Hubertus <hvandam at bnl.gov> wrote:

> Hi Tram Danh,
>
> For Autodock you can find some information in this posting:
>
> http://autodock.scripps.edu/faqs-help/how-to/adding-new-atom-parameters-to-autodock
> A rather extended set of parameters is given in (including At):
>
> http://autodock.1369657.n2.nabble.com/ADL-Parameters-for-docking-with-metal-ions-in-receptor-td2505649.html
> However, no references are given for the data used to obtain these
> parameters. So I am not sure how much you can trust this.
>
> Best wishes,
>
>     Huub
>
>
> -----------------------------------------------------------------------------------------------------
> Hubertus van Dam, 631-344-6020, hvandam at bnl.gov
> Brookhaven National Laboratory
>
>
> On 8/11/20, 16:32, "autodock-bounces at scripps.edu on behalf of Tram B.
> Danh" <autodock-bounces at scripps.edu on behalf of 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:
>     >
>     >
> https://urldefense.com/v3/__http://autodock.scripps.edu/faqs-help/faq/missing-atom-types-201cwhy-atom-type-x-is-not-recognized-201d__;!!P4SdNyxKAPE!X5JOkkL8agv15ymnaIfrO89BbdJIqAsIV_02qn6C7Lt7iKabF1V3uaET0xESUoo$
>     >
>     > 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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