ADL: Generate ligands pdbqt in batch mode

Gianluca Interlandi gianluca at
Mon Oct 5 19:37:54 PDT 2020

Dear all,

I have learned to use AutoDock Vina to dock a ligand on a receptor. I used 
ADT to create a pdbqt file from the ligand mol2 file. I need to do the 
same for a few thousand ligands, which are individually stored as mol2 
files. I started `raccoon` from the MGLTools package for Linux. I have the 
option to connect to a server, but the ligand files are on my workstation. 
The button for "Workstation" is grayed out and cannot click on it. How can 
I use raccoon to convert all mol2 files in a folder to pdbqt?

I also tried using openbabel, but the pdbqt file produced for a test file 
is different than the one produced by ADT. Is there a way to run ADT in 
batch mode?



Gianluca Interlandi, PhD gianluca at
                     +1 (206) 685 4435

Research Assistant Professor at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.

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