ADL: Adding heavy metal ions
forli at scripps.edu
Wed Mar 9 12:52:13 PST 2016
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
and the corresponding files here:
Hope this helps.
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?
> 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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email: forli at scripps.edu
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