2018 Denovo design tutorial 1 with PDB 2NNQ
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Contents
2018 Denovo design tutorial 1 with PDB 2NNQ
Files Needed
Fragment Libraries
A focused fragment library will be used in this tutorial, in order to attempt building the same ligand. A focused fragment library can be generated using the same ligand.
Create a new directory for the fragment library.
mkdir fraglib
Inside the fraglib directory create a new input file for fragment generation.
Focused Denovo Growth
conformer_search_type flex write_fragment_libraries yes fragment_library_prefix fraglib fragment_library_freq_cutoff 1 fragment_library_sort_method freq fragment_library_trans_origin no use_internal_energy no ligand_atom_file ./candidate_mol_gen_frag.mol2 limit_max_ligands no skip_molecule no read_mol_solvation no calculate_rmsd no use_database_filter no orient_ligand no bump_filter no score_molecules no atom_model all vdw_defn_file ../../../dock/box/vdw_AMBER_parm99.defn flex_defn_file ../../../dock/dock/flex.defn flex_drive_file ../../../dock/dock/flex_drive.tbl ligand_outfile_prefix output write_orientations no num_scored_conformers 1 rank_ligands no
