bio-otto / autodock-vina_scripts

Autodock vina command line scripts

Autodock vina docking scripts

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docking.sh

How it works?

1. When you run the docking.sh for the first time it checks if the folder named results exist. If it is exist then it counts the result count in the folder for the further usage. If it doesn't exist then it creates results folder.
   • results folder is the location of where the console output of Autodock vina will be save.
2. Then it checks the existence of results_table.csv file. If it doesnt exist it creates one.
   • results_table.csv is the where the summary of results will be save (Number of result, Lowest affinity value, Average value of 'dist from rmsd', Maximum value of 'dist from rmsd', Seed number, etc.).
3. Then it detects the config file. Config file must be named as (some_name)_conf.txt (Check config file). PS: Be sure that there is not file contains _conf.txt in the name.
4. Then it starts to work until it reaches the 'maxattempt' number which you entered at the top of docking.sh line.
5. Script prints the summary of the result (Average value of 'dist from rmsd', Maximum value of 'dist from rmsd', Lowest affinity value) and it stores the detailed information in the results_table.csv table.
6. When process is finished. You can check the results_table.csv for the value you want to find. When you find the result, you can copy the seed number of result and then run the vina with the seed you copied to reach result that you want.

Example workflow

1. Open the terminal in the docking folder. Docking folder must be contains ((some_name)_conf.txt, protein.pdbqt file, ligand.pdbqt file which you defined in the config file (Check config file).
2. Then edit the maxattempt number in the docking.sh as you want.
3. Then type ./docking.sh in the terminal. It must be give a output like <result_number> started... that means script is working.
4. If you see Process finished that means script is finished working. You can check the results_table.csv for the pick result for the seed.
5. Then run vina --config test_conf.txt --seed <seed_number>

Example config file

receptor= protein.pdbqt
ligand= SO.pdbqt

center_x= 4.402
center_y= -8.060
center_z= 8.874

size_x= 66
size_y= 56
size_z= 54

out= vina_outSO.pdbqt
log= logSO.txt

exhaustiveness= 8

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