i'm carrying out molecular docking for a compound containing metal, Platinum, with 3T6A protein using Autodock 4.2.6 tool. However, i cannot run Autogrid to obtain .dpf file which i'm going to used for Autodock to obtain .dlg file
Hi. Maybe you need to give us the error/warning remark when running the autogrid. But I guess it is because you use undefined metal atoms in your structure. You can go to the link https://autodock.scripps.edu/how-to-add-new-atom-types-to-the-autodock-force-field/ to add platinum atom parameter and solve this
Rezi Riadhi Syahdi thanks for your help. But sadly i cannot find for platinum in the link you provided. I'm sharing you my .gpf file which i used for Autogrid run. Hoping for your further help
atom_par Pt 2.75 0.080 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
maybe this will be useful for you
Rezi Riadhi Syahdi "atom_par Pt 2.75 0.080 12.000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding" where should I put this, in which file?
add the line to the AD4.1_bound.dat files and also you need to add the line
parameter_file
to the gpf file
Please refer to the web page I mentioned in my first answer
Rezi Riadhi Syahdi thank you so much!
Now, I can carry out the Docking.
You can use MultiDock Screening Tool https://yogeshgaikwad-labhelper.github.io/multidockweb.github.io/index.html
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