How can ligand pdbqt input files to AutoDock 4 be batched?

ccsb-scripps / AutoDock-Vina

AutoDock Vina

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How can ligand pdbqt input files to AutoDock 4 be batched? #224

Open YoavShamir5 opened 1 year ago

YoavShamir5 commented 1 year ago

Hi,

I am using AutoDock 4 for covalent docking. I wonder - is it possible to provide as input a pdbqt file with multiple ligands included, and later parse the dlg output accordingly? If so - what main modifications are required to the docking process, and is there a tutorial (or examples of the format of the batched pdbqt input and output files) available? Thanks!!

diogomart commented 1 year ago

Hi,

autodock4, vina, and autodock-gpu expect one molecule in each pdbqt. But vina and autodock-gpu have batching capabilities, see the --batch option in the vina docs and the filelist option in autodock-gpu's README file.