How to use autodock-GPU for covalent docking in batch mode?

[Yongrui-Wang]

Hi！ In [https://github.com/ccsb-scripps/AutoDock-Vina/issues/80#issuecomment-1019534197] As mentioned in the link, it seems that autodock-gpu can already do covalent docking, but I don't know how to do it. Can you provide some tutorials? Thanks！

[Thanh-An-Pham]

Hi！ In [https://github.com/[ccsb-scripps/AutoDock-Vina/issues/80](https://github.com/ccsb-scripps/AutoDock-Vina/issues/80)#issuecomment-1019534197] As mentioned in the link, it seems that autodock-gpu can already do covalent docking, but I don't know how to do it. Can you provide some tutorials? Thanks！

I got the same problem too, do you have the solution yet? Many thanks ^^

[diogomart]

Maybe meeko can help, see docking covalent ligands as flexible sidechains.

[Thanh-An-Pham]

Maybe meeko can help, see docking covalent ligands as flexible sidechains.

Thank for your help! I have manage to run the mk_preprare_ligand.py succesfully but what should I do next? I have tried process the file with prepare_flexreceptor4.py of MGLTools as instruction of Covalent Docking (Autodock4) but it didn't work . The code is below and the method i use is example of covalentdock in meeko !/usr/local/Meeko/scripts/mk_prepare_ligand.py\ -i ligand_including_cys_sidechain.sdf\ --receptor protein.pdb\ --rec_residue ":CYS:6"\ --tether_smarts "NC(=O)C(O)(C)SCC"\ --tether_smarts_indices 9 8\ -o prepared.pdbqt Return: /usr/local/Meeko/example/covalent_docking @> 397 atoms and 1 coordinate set(s) were parsed in 0.01s. CovalentBuilder> searching for residue: resname CYS and resnum 6 and (name CA or name CB) !/usr/local/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_flexreceptor4.py -r prepared_ligand.pdbqt -s prepared_ligand::CYS6 Return: no residue found using string prepared_ligand::CYS6 Best Regard!