Hello and thank you for the great tool!
It seems that currently PLACER is expecting a preconstructed protein-ligand complex. Then, the docked pose of a ligand is used to define the binding pocket. Finally, both the docked pose and up to ~600 atoms around it are optimized in a fully flexible way.
What if I want to dock a ligand into a novel pocket/location which is outside the current docked pose? How can I specify the new binding site manually, e.g. by selecting particular target residues? I tried to use --corruption_centers and --crop_centers for the purpose of defining the target binding residues, but in both cases I get the following error:
networkx.exception.NodeNotFound: Source ('B', 1, 'LIG', 'C21') is not in G
which means that the pocket is selected as I want, but the ligand coordinates from the input file are not present inside the pocket (obviously, because I want to redock the pose into a new site).
Classical docking programs require protein and ligand as separate files and a pocket definition, i.e. a pre-docked ligand pose it usually not needed. So, is there a way to use PLACER as a classical docking engine?
E.g., can I submit a protein and ligand #1 complex in one PDB, use ligand #1 to define the target site, but then also provide ligand #2 for docking itself?
Or, can I submit a protein and a ligand and select the binding site by providing a list of specific residues?
Thank you very much for your work and your time!
Hello and thank you for the great tool!
It seems that currently PLACER is expecting a preconstructed protein-ligand complex. Then, the docked pose of a ligand is used to define the binding pocket. Finally, both the docked pose and up to ~600 atoms around it are optimized in a fully flexible way.
What if I want to dock a ligand into a novel pocket/location which is outside the current docked pose? How can I specify the new binding site manually, e.g. by selecting particular target residues? I tried to use --corruption_centers and --crop_centers for the purpose of defining the target binding residues, but in both cases I get the following error:
networkx.exception.NodeNotFound: Source ('B', 1, 'LIG', 'C21') is not in Gwhich means that the pocket is selected as I want, but the ligand coordinates from the input file are not present inside the pocket (obviously, because I want to redock the pose into a new site).
Classical docking programs require protein and ligand as separate files and a pocket definition, i.e. a pre-docked ligand pose it usually not needed. So, is there a way to use PLACER as a classical docking engine?
E.g., can I submit a protein and ligand #1 complex in one PDB, use ligand #1 to define the target site, but then also provide ligand #2 for docking itself?
Or, can I submit a protein and a ligand and select the binding site by providing a list of specific residues?
Thank you very much for your work and your time!