ADL: metal docking

Van Dam, Hubertus hvandam at bnl.gov
Tue Oct 13 13:18:22 PDT 2020


Hi,
To add metal ions to the Autodock parameter set have a look at:
http://autodock.scripps.edu/faqs-help/how-to/adding-new-atom-parameters-to-autodock
Alternatively there are a whole bunch of parameters available here:
http://autodock.1369657.n2.nabble.com/ADL-Parameters-for-docking-with-metal-ions-in-receptor-td2505649.html
One thing to consider is that usually you have a protein target and you dock many drug candidates to it. In your case you have one metal ion and you want to know where it binds to what protein. In that case you might have other methods available to you. I would guess that docking will just give binding based on the electrostatic interaction. 
Best wishes,
Huub

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

On 10/10/20, 12:20, "autodock-bounces at scripps.edu on behalf of Dhruvi Mehta" <autodock-bounces at scripps.edu on behalf of dhruvilalitmehta at gmail.com> wrote:

    Hello,
    I am a student and learning docking for a research project to be
    submitted in my institution as a part of my grades.
    I want to dock cadmium against proteins of my choice but I got to know
    that there are some parameters that are to be set for metal docking.
    Could you please help me with what those parameters are for cadmium metal ?

    Thank you


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