ADL: Problem with AutoDock Vina Modeling

Van Dam, Hubertus hvandam at bnl.gov
Wed Aug 12 19:12:16 PDT 2020


Hi Tram Danh,

The parameters in Autodock are also hardcoded (although you should be able to read the parameters from a file at run time as well). The parameters are given in the files AD4_parameters.dat and AD4.1_bound.dat. However these files are converted with paramdat2h.csh into the default_parameters.h header file, which is included in read_parameter_library.cc. So, to incorporate these parameters into your executable you will have to recompile your code after you changed the parameter files.

Best wishes,

    Huub

-----------------------------------------------------------------------------------------------------
Hubertus van Dam, 631-344-6020, hvandam at bnl.gov
Brookhaven National Laboratory
 

On 8/12/20, 19:43, "autodock-bounces at scripps.edu on behalf of Tram B. Danh" <autodock-bounces at scripps.edu on behalf of 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:
    >
    > https://urldefense.com/v3/__http://autodock.scripps.edu/faqs-help/how-to/adding-new-atom-parameters-to-autodock__;!!P4SdNyxKAPE!S7eKQqy8yNTjYCWfGnIj5f0e_dKz__MZBBUU4tkYsHUELdZPHoJ3CptUGqLn-o8$ 
    > A rather extended set of parameters is given in (including At):
    >
    > https://urldefense.com/v3/__http://autodock.1369657.n2.nabble.com/ADL-Parameters-for-docking-with-metal-ions-in-receptor-td2505649.html__;!!P4SdNyxKAPE!S7eKQqy8yNTjYCWfGnIj5f0e_dKz__MZBBUU4tkYsHUELdZPHoJ3CptUSDg2yQQ$ 
    > 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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