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Only flexible sidechain docking
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Author:  meny [ Thu Oct 20, 2016 7:53 am ]
Post subject:  Only flexible sidechain docking


I'm trying to perform a flexible sidechain docking where the ligand is covalently bonded to the protein. <the method was successfully used in: Giulia Bianco, Stefano Forli David S. Goodsell and Arthur J. Olson; PROTEIN SCIENCE 2016 VOL 25:295—301. However, I did not manage to carry out the calculation with AutoDock 4. The program doesn't reads in the atoms that need to be moved if only the flexible residue is given as *.pdbqt input (besides the rigid part of the macromolecule). Specifying an empty *.pdbqt file as input with the move command (along with flexres *.pdbqt) lets AutoDock 4 read in the flexible residues but it does not move them. Specifying the flexible residue as the ligand results in chemically meaningless conformations.

I would appreciate any help with this problem!

Best regards,

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