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ccsb-scripps / AutoDock-Vina

AutoDock Vina
http://vina.scripps.edu
Apache License 2.0
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about covalent docking #80

Open debanjansen48 opened 2 years ago

debanjansen48 commented 2 years ago

is it possible to perform covalent docking with vina 1.2.3 and covalent docking based virtual screening (batch file mode)?

can I install this tool (vina 1.2.3) in windows ?

diogomart commented 2 years ago

Unfortunately no, because the batch mode works only for the ligands, and covalent docking passes the ligand as a flexible sidechain.

Soon, it will be possible to do covalent docking in AutoDock-GPU, in batch mode, after this pull request is completed: https://github.com/ccsb-scripps/AutoDock-GPU/pull/171/

debanjansen48 commented 2 years ago

Thanks for the information. The covalent docking with autodock 4.2 contain some scripts written in python 2. Recent linux OS possess python 3. Therefore these scripts depicts issue. I changed the print statement syntex as per python 3 (only add () and use import pybel as ob ) and found most of the scripts started working. But unable to solve one issue associated with class OBMolCopy(ob.OBMol). the actual error is "Class OBMolCopy(ob.OBMol): AttributeError: module 'pybel' has no attribute 'OBMol"

Autodock 4.2 is one of the most reliable open source docking tool. Therefore in my covalent docking project I want to use it. But encountered by above issue. Can you assist me to resolve it. I am attaching the changed scripts as .txt documents. Thanks Sir

CopyMol.txt py-3-prepareCovalent.txt ResidueProfiler.txt