ADL: Problem with AutoDock Vina Modeling

Tram B. Danh tbdanh at uci.edu
Thu Aug 13 14:40:42 PDT 2020


Hi Leandro,

Thank you for your explanations! I’ve created At in the existing parameter
file but AutoDock still couldn’t recognize At. Can you explain how to
compile Vina with the new parameters?

Thank you,
Tram Danh

On Wed, Aug 12, 2020 at 6:06 PM Leandro Bortot <leandro.obt at gmail.com>
wrote:

> Hello Tram,
>
>      The parameters for Vina are hardcoded, which means that you need to
> get the source code, make your modifications and recompile vina from
> source.
>      Specifically, the parameters are in src/lib/atom_constants.h.
>
>      A good way to derive your parameters would be to create the new At
> atom type using the existing parameters for I and making the appropriate
> changes such as increasing its radius.
>      After doing this, you need to compile Vina with the new parameters.
>      Finally, you can validate your parameters by performing docking
> calculations and comparing your results with experimental data. It may be
> hard to get experimental data for molecular interactions with At-containing
> molecules, but maybe your research group has something.
>
>      Another way, which isn't so polished but is way easier and that may be
> useful to give you some insights, is to just change At to I in your
> molecules. Vina will perform the docking since it already knows I. However,
> you have to carefully take this (arguably big) "approximation" into
> consideration when interpreting and discussing your results, especially if
> there are direct protein-At contacts (assuming you are performing
> protein-ligand dockings).
>
> I hope it helps,
> Leandro
> -------
> Leandro Oliveira Bortot
> Postdoctoral Fellow
> <http://linkedin.com> https://www.linkedin.com/in/leandro-obt/
> Laboratory of Computational Biology
> Brazilian Biosciences National Laboratory (LNBio)
> Brazilian Center for Research in Energy and Materials (CNPEM)
> Zip Code 13083-970, Campinas, São Paulo, Brazil.
>
>
>
> On Wed, Aug 12, 2020 at 8:42 PM Tram B. Danh <tbdanh at uci.edu> wrote:
>
> > 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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