ADL: Add a new atom to AutoDock

Diogo Martins diogo.stmart at gmail.com
Thu Aug 27 00:26:14 PDT 2020


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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