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ccsb-scripps / AutoDock-GPU

AutoDock for GPUs and other accelerators
https://ccsb.scripps.edu/autodock
GNU General Public License v2.0
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Flexible Residue Positions when Ligand is Docked #197

Closed Professor333 closed 2 years ago

Professor333 commented 2 years ago

When performing flexible docking, and with --gbest enabled, is there a way to output the positions of the flexible residues as they are found with the Ligand docked?

Does the --npdb flag output the top # hits? As in, --npdb 5 would output the top 5 best poses? Again, would there be a way to output the positions of flexible residues for each pose?

Thanks for any help

atillack commented 2 years ago

@Professor333 "Best", similarly to --gbest, in the context of --npdb refers to the scoring function value, not the estimated free binding energy (which is what the dlg output data tables and clustering analysis is sorted by).

--npdb 5 would output the 5 top scoring poses for each run.

Currently, its output does not contain the flexible residue atoms but it's a feature I can add in a future PR.

Professor333 commented 2 years ago

Thank you for adding this feature. Much appreciated.