I try to understand how to generate a new collection starting from the best poses for a second run.
I don’t know if it exists a specific script to do that.
I am able to extract the best poses.
I am able to use vfvs_prepare_new_collections2.sh from a classic input file and generate a tranch archive from the best ligands.
But I am not able to use vfvs_prepare_new_collections.sh starting from a ligand file with the first column the collection and the second column the ligand name (it is perhaps one key for my problem). Impossible to run this script. I don’t really understand what should be the ligand file (the same than for the extraction of the best poses (vfvs-pp_extract_best_poses.sh) ?) and the pdbqt_input_folder
Thank you for your help.