Setting up docking of multiple ligands

[victorhellgren]

I'm wondering if there is an option to make AMDock automatically dock multiple ligands after each other with Autodock4Zn. I'm going to dock 200 ligands and I don't want to start a new project and check all the boxes and everything with every new ligand since that would take forever. Is there any way to do this?

Kind regards,

Victor Hellgren
MSc in Organic Chemistry, Uppsala University

[Valdes-Tresanco-MS]

Unfortunately not. AMDock in its current version only supports one ligand at a time. We are working on a new version, but it may take some time

[victorhellgren]

I understand! Very good job with the program, it makes everything so much easier than using the command prompt and when the new version hits it will be fantastic! I was thinking though if there was a way to maybe automate it using an external software which could insert all the parameters automatically, like a bot or something.

[Valdes-Tresanco-MS]

Those procedures can be more complex than running multiple scripts. I recommend you check out the AutoDock4Zn tutorial.

You could do the following:
With AMDock

• Prepare the protein (proton, generate the pdbqt, add the dummy atom TZ )
• Determine the dimensions and position of the box

Scritp Bash that iterates over the directories of the ligands

• prepare the ligands
• generate the gpf
• run autogrid
• generate the dpf
• run the autodock4

The new version is going to be loaded with new features, but the change from python2 to python3 and other issues have been a bit long and tedious. We regret that the current version is not sufficient.

[leehiufung911]

Hello, I am also looking to see if I can dock multiple ligands.
I was wondering if this was ever implemented? (Either Linux or Windows version)

[Valdes-Tresanco-MS]

@leehiufung911 Unfortunately no. We desire to do it, to implement all the characteristics that we have planned. However, without financing, there is no way. We have had to focus on other important projects and leave AMDock a little behind. I hope to get back to it sooner rather than later.