Difference between revisions of "2018 Denovo design tutorial 1 with PDB 2NNQ"
From Rizzo_Lab
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==Focused Denovo Growth== | ==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 | ||
==Focused Denovo Rescore== | ==Focused Denovo Rescore== | ||
Revision as of 15:51, 21 February 2018
Contents
2018 Denovo design tutorial 1 with PDB 2NNQ
Files Needed
Fragment Libraries
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
