ADL: Add a new atom to AutoDock

Van Dam, Hubertus hvandam at bnl.gov
Thu Aug 27 12:23:30 PDT 2020


Hi Tram,

You'll find the .dpf file where you created it with the 

	prepare_dpf42.py

script. The .gpf file is created with the

	prepare_gpf4.py

script and it depends on you where you put it.

Best wishes,

     Huub

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

On 8/27/20, 13:39, "autodock-bounces at scripps.edu on behalf of Tram B. Danh" <autodock-bounces at scripps.edu on behalf of tbdanh at uci.edu> wrote:

    Where can I find .dpf or .gpf files?

    Thanks for your help!

    On Thu, Aug 27, 2020 at 12:28 AM Diogo Martins <diogo.stmart at gmail.com>
    wrote:

    > Hi Huub, Tram,
    >
    >
    >
    > New parameters for autodock4.2 can be incorporated without re-compiling the
    >
    > program, by adding "parameter_file modpars.dat" as the first line in the
    >
    > docking parameter file (.dpf).
    >
    >
    >
    > Best regards,
    >
    >
    >
    > On Wed, 26 Aug 2020 at 20:01, Van Dam, Hubertus <hvandam at bnl.gov> wrote:
    >
    >
    >
    > > Hi Tram Danh,
    >
    > >
    >
    > > The parameters in Autodock are 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 8/26/20, 17:28, "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'm trying to add Astatine (At) to AutoDock. I've added values for At
    >
    > > in
    >
    > >     the parameter file, but I've struggled with directing AutoDock to use
    >
    > > this
    >
    > >     modified file instead of the default one. If possible, please explain
    >
    > > how
    >
    > >     to perform this step.
    >
    > >
    >
    > >     Thank you for your help!
    >
    > >     Tram
    >
    > >     ________________________________________________
    >
    > >     --- ADL: AutoDock List  ---
    >
    > >
    > https://urldefense.com/v3/__http://autodock.scripps.edu/mailing_list__;!!P4SdNyxKAPE!Xtsz5m0J_VRG0P3EMq_tHww4E6kRQwmvs9TZ8Ft0ZRmEw2MHjYvM8t3P2jZcNZk$
    >
    > > ---
    >
    > >
    >
    > >
    >
    > >
    >
    > > ________________________________________________
    >
    > > --- ADL: AutoDock List  --- https://urldefense.com/v3/__http://autodock.scripps.edu/mailing_list__;!!P4SdNyxKAPE!Q4SbvtzeigJk5qtmWPnuM-JJh7wClbDB5l9Qr00D6Mn6mE908JWJTC-5KXJ1tQE$  ---
    >
    > ________________________________________________
    >
    > --- ADL: AutoDock List  --- https://urldefense.com/v3/__http://autodock.scripps.edu/mailing_list__;!!P4SdNyxKAPE!Q4SbvtzeigJk5qtmWPnuM-JJh7wClbDB5l9Qr00D6Mn6mE908JWJTC-5KXJ1tQE$  ---
    ________________________________________________
    --- ADL: AutoDock List  --- https://urldefense.com/v3/__http://autodock.scripps.edu/mailing_list__;!!P4SdNyxKAPE!Q4SbvtzeigJk5qtmWPnuM-JJh7wClbDB5l9Qr00D6Mn6mE908JWJTC-5KXJ1tQE$  ---




More information about the autodock mailing list