ADL: Reg metal ligands

Van Dam, Hubertus hvandam at bnl.gov
Tue Dec 22 08:29:33 PST 2020


Hi,

I think the easiest is to add the data to the *.dat files in the autodock source code directory. The file names are:
- AD4.1_bound.dat
- AD4.1_compact.dat  
- AD4.1_extended.dat  
- AD4_parameters.dat  
- AD4_PARM99.dat
A subsequent recompile of the code will regenerate the "default_parameters.h" file and integrate the parameters into the executable (both for autodock and autogrid). More information about this works can be found in the file:

	src/autodock/README (section "Configuration notes")

Alternatively you can specify a file with parameters on the command line with the "-p" flag, e.g.

	autodock -p <DOCKPARMFILE>

As to what values to include in the parameter files that is a different story. See:
- http://autodock.scripps.edu/faqs-help/how-to/adding-new-atom-parameters-to-autodock
I have also found an example of a parameter set with many metal atoms at:
- http://autodock.1369657.n2.nabble.com/ADL-Parameters-for-docking-with-metal-ions-in-receptor-td2505649.html
However, I have no idea how good these parameters are. 

Best wishes,

    Huub

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

On 12/21/20, 23:17, "autodock-bounces at scripps.edu on behalf of jambu lingam" <autodock-bounces at scripps.edu on behalf of jambulingam48 at gmail.com> wrote:

    Dear sir

    Kindly explain how to include parameters file in grid and docking such
    as..metal like mn cu and co
    Thanking you
    Jambulingam
    Asst professor
    The erode college of pharmacy
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