ADL: Problem with AutoDock Vina Modeling

Diogo Martins diogo.stmart at gmail.com
Tue Aug 18 15:28:01 PDT 2020


Hi Tram,

In Vina, you'll need to modify both "atom_constants.h" and "model.cpp". In
this commit diff you can see all the lines that must be changed to support
a new atom type:
https://github.com/ccsb-scripps/vina-astatine/commit/3b87cd88f60f7bd6cce4b2090bc97169668f1ba6


In this example I set the following parameters for "At":
 - covalent radius = 1.44
 - vdW radius = 2.3

The only terms that will apply to "At" are repulsion, gauss1 and gauss2. If
you want the hydrophobic term then XS_TYPE_At_H needs to be added to
xs_is_hydrophobic() in atom_constants.h.

This vina version compiles in linux and Mac using recent Boost libraries.

Hope this helps,

On Tue, 18 Aug 2020 at 12:05, Tram B. Danh <tbdanh at uci.edu> wrote:

> Hi Leandro,
>
> Could you check to see if this is the most current file that I need to
> modify?
>
> http://vina.scripps.edu/download/autodock_vina_1_1_2/src/lib/atom_constants.h
>
>
> I couldn't find "src/lib/atom_constants.h" file in my C drive, but I looked
> it up on the web.
>
> Thank you,
> Tram
>
> On Thu, Aug 13, 2020 at 4:28 PM Leandro Bortot <leandro.obt at gmail.com>
> wrote:
>
> > Hello Tram,
> >
> >      There are instructions about the compilation process at Vina's
> > website: http://vina.scripps.edu/manual.html#build
> >      I've never done that myself with Vina, so I can't give you any other
> > specific help. I suggest that first you try compiling Vina without
> > modifications just to be sure about the process and then proceed to
> compile
> > Vina with the new parameters.
> >
> > Cheers,
> > 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 Thu, Aug 13, 2020 at 6:43 PM Tram B. Danh <tbdanh at uci.edu> wrote:
> >
> > > 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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> > > > >
> > > >
> > >
> >
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> >
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