While docking SiO2 with a receptor protein in Autodock vina, the software threw an error which says "Si" is not a valid Autodock type. What is the possible reason and how to rectify this. How can we dock such compounds with a protein to see if we can use them in their nanoparticles form to inhibit the protein function?
Thanks in advance.
Regards,
Vinay
This arise due to lack of Si parameter.
Try using PyRx (uses Autodock vina)
The parameters for Si are mentioned below
atom_par Si 4.30 0.402 12.175 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
Copy and paste in the AD4_parameter.dat file. (align the values correctly). Next, you need to keep the modified bat file to the folder where the autodock.exe and autogrid.exe files are. Then you need to modify the .gpf and .dpf files by adding "parameter_file AD4_parameters.dat" command as shown in the attached screenshot.
Happy docking !!!
Dear Vinay Mohan Kandpal,
The contributions of prof. Faizul Azam is more than enough to inform the discussion. you have to add the Silicon atom parameter manually in AD4_parameter.dat file and edit the both glg as well as dlg file (mention above) and run again.
I have attempted to implement these changes to the proper files for boron but Have continued to be unsuccessful. Do these changes have to be made in auto dock tools? If not how can I make the program directly read the altered atom parameter file? Or are there files to altered that were apart of to auto dock vina that I cannot access? Any help would be appreciate! Thank you!
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