molecular docking for a ligand to multi protein
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10 months ago
iamsmor • 0

Hello everyone

I am new in molecular docking. I have a ligand and I would like to try docking with many proteins but I only know to do it one by one. Is there any guide or tutorial or something etc that I can get information?

Thanks for any help

molecular-docking autodock-vina • 666 views
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If you have already prepared the protein and ligand, then to avoid running the command for multiple times. You can use "For" or "while" loop in the command line.

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thank you ı tried but ı am confised about how ı wil arrange or add line for the config.txt in script file. Because I havent prepared config.txt for all protein. I have only grid.txt

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Hey, Its a long way to make the script. I can give some approaches. Make an array in tabular format for each variable and use for loop with "awk" (to read columns), then "cat" (to read each line of your array file). In the end assign the variable values in the config file.

Example config.txt

receptor = protein.pdbqt ligand = ligand.pdbqt

center_x = center_y = center_z =

size_x = size_y = size_z = out= vina_out.pdbqt log= log.txt Energy_range = 4

exhaustiveness = 8

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