A useful script for AutoDock4 and Vina that merges flexible and rigid PDBQT output

AdutoDock and AutoDock Vina are popular programs for molecular docking developed by the Molecular Graphics Lab at The Scripps Research Institute. From AutoDock4 it is possible to allow certain side-chain flexibility to the residues of the binding pocket. For accomplishing this, AD and AD Vina produce a flexible-residues file in PDBQT format which is separated from the rest of the protein, stored in a separated PDBQT file containing only the rigid residues. We have not found, available in the public domain, a trivial method for re-merging in a consistent way the PDBQT output containing the flexible residues and the PDBQT input containing the rest of the protein.We have therefore developed a tiny bash script that performs exactly that merging operation. More information on how the script works can be obtained by viewing the contents of the script in a text editor. The script, which it is pretty much self-explanatory, can be downloaded by clicking on the following link: flexrigidpdbqt2pdb.



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