You should go for High through put docking study. Use GOLD (https://www.ccdc.cam.ac.uk/solutions/csd-discovery/components/gold/) or Glide (https://www.schrodinger.com/glide). Thanks.

Hi,

You can use Pyrx software for your aim

Yes, it is absolutely possible - you'll have to use the command line though, I don't think it'll work with any of the graphical interfaces I've seen. It is easier with Vina than 4.0, since you no longer need grid files and such, but even with 4.0 it's possible if you set up enough grids in advance.

My workflow in the past has been to draw in or download a dataset (these days, probably from Zinc, and probably as an sdf file), use Babel/oBabel to convert the mass file into individual pdb files. Next, I use the command 'ls -1 > moleculeList.txt' to get a single column list of the molecules in a text file. I set up a file 'config.txt' to contain all the information for the protein/docking scenario other than the specific ligand. Finally, I set up a script to run in Cygwin (on windows) or a bash terminal (on linux).

An example config.txt:

receptor = protein.pdbqt

center_x = -0.809

center_y = -4.028

center_z = 19.32

size_x = 22

size_y = 16

size_z = 22

exhaustiveness=3

cpu = 3

An example script:

FOR /F "tokens=1,2 delims=." %%A IN (moleculeList.txt) DO (

echo %%A.%%B

prepare_ligand4.py -l %%A.pdb -o %%A.pdbqt -A bonds_hydrogens

vina --ligand %%A.pdbqt --config config.txt --out .\Solutions\%%A_vinaDocked.pdbqt

)

Note that prepare_ligand4.py is, I believe, part of the Autodock tools package. I THINK you can skip that step, and that Vina will deal with pdb files, but I'm not positive. Either way, this script is set to save all your output to a separate directory, so you can just look in that directory to see how many solutions you've got. If the program crashes, or you suffer a power outage, you can just look at the most recent solution, delete all the inputs from 'moleculeList.txt' that are already complete, and restart the process, just working on molecules you haven't looked at yet.

For Autodock 4.0, compared to Vina, there's more protein prep to do, and in particular atom-specific grid files. I recommend just making a grid file for every atom used in organic chemistry, up to and including iodine and bromine and such, unless you know for a fact those atoms aren't in your dataset, since if a grid file is missing, the process will just crash.

@ William P Katt

this script is to be used in bash /linux or windows sir? Actually I am working with windows. You are also mentioning to male a txt file for the list of molecules that I didnt understand. Do u have any video/PDF tutorial for that sir? Thanks

Actually, looking at it, I think I made this script to work in a command window in Windows, though you could have a similar script for bash or linux. For molecule list, I typically do use linux/Cygwin, but you can do the same with the dir command: navigate to the directory with your files, and type "dir /b *.pdb > moleculeList.txt"

Note that you'll have to change "*.pdb" to something else if you choose to use a different file format.

Afraid I don't have a video tutorial, but this is all the steps you should need. Once you have moleculeList.txt and config.txt set up, just copy the script I provided into a file (say "runDocking.bat"), then from your command line, type "./runDocking.bat". It should start running Vina for you.