Shifted coordinates in resulting .pdbqt and .pdb files

Computer-Aided Drug Design at the Durrant Lab Forums AutoGrow4 Shifted coordinates in resulting .pdbqt and .pdb files

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    • #35318

      Hello everyone,

      I was able to run Autogrow to completion, finding several molecules with improved affinity for my target. Now I’m trying to predict the interactions between the new candidates and my receptor.

      However, once I decompressed the files and tried to open both my receptor and one the resulting .pdbqt files, the ligand isn’t inside the gridbox defined for my receptor.

      I’ve double checked that the receptor I’m opening is the same as the one used in the run and that the gridbox defined in the .json file was correct.

      I believe that some sort of transformation in the coordinates happened at some point after the docking with the ligands, or with the receptor prior to the docking.

      Either way, I’m unable to view the complex of my new ligands with my receptor. Is this some sort of bug or am I missing something here?

      Thanks for the help!

    • #37847
      Jacob Durrant

      Hi Patricio. Please forgive my delay in responding. I believe AutoGrow actually redocks the compounds with every generation by default. I suspect the file you’re seeing is the predocked ligand. I’d recommend redocking that compound back into the receptor using AutoDock Vina or some other program, independent of AutoGrow. I hope this answer helps. ~Jacob

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