ADL: Add a new atom to AutoDock

Tram B. Danh tbdanh at uci.edu
Thu Aug 27 10:35:17 PDT 2020


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
>
> >     ________________________________________________
>
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>
> >
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>
> > ---
>
> >
>
> >
>
> >
>
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>
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>
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