ADL: Adding heavy metal ions

Stefano Forli forli at scripps.edu
Wed Mar 9 12:52:13 PST 2016


Hi John,
the instructions on how to use a customized parameter file are described in the user manual.
You can take a look at pages 31 and 39 for AutoGrid and AutoDock, respectively.
Although, if you use the latest AutoDock4 version (v.4.2.6) at least zinc should be 
already in the standard parameter file.

Also, if you are interested in better zinc coordination parameters, you should look at 
this publication:

   http://pubs.acs.org/doi/abs/10.1021/ci500209e

and the corresponding files here:

   http://autodock.scripps.edu/resources/autodockzn-forcefield

Hope this helps.
Happy dockings!

S

On 03/09/2016 04:55 AM, Beale, John wrote:
> Good morning,
>
> I sent a message earlier this morning asking how to add parameters to all of the GPF and DPF files. Well, I figured out how to do that. According to the Autodock webpage, the final step is to inform Autodock that it should use the modified parameters instead of the default ones in the program.
>
> Can someone tell me how to do this?
>
> Thanks!
>
>
> John M. Beale, Jr.
> John M. Beale, Jr., Ph.D.
> Professor of Medicinal Chemistry and Pharmacognosy
> Saint Louis College of Pharmacy
> 4588 Parkview Place
> Saint Louis, Missouri  63110-1088
> Office: 314-446-8461
> Cell: 314-315-0409
> FAX: 314-446-8460
> John.Beale at stlcop.edu<mailto:John.Beale at stlcop.edu>
>
> ________________________________________________
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>

-- 

  Stefano Forli, PhD

  Assistant Professor of Integrative
  Structural and Computational Biology,
  Molecular Graphics Laboratory

  Dept. of Integrative Structural
   and Computational Biology, MB-112A
  The Scripps Research Institute
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