I get the following error messages after running the simulation:
Sorry, there are no Gasteiger parameters available for atom ligandx.ligand:A:lig1:O7
AutoDock Vina ligand docking initiated for 4y00.pdb
Running AutoDock Vina for 4y00.pdb failed; see Reply Log for information
Application stderr
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Parse error on line 102 in the file "ligand.pdbqt": Atom 45 has not been found in this branch
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Application stdout
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Prepare your ligand using AutoDock (where you can add Gasteiger charges to the ligand) and covert it into .pdbqt format.
Thank you all for your help. I was able to get around the error by using another program (PyRx) over UCSF Chimera. The latter was giving me the unexplained error, but I was able to simulate docking with PyRx successfully. It also helped that the ligand be downloaded in .sdf format.
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