Difference between revisions of "2018 Denovo design tutorial 1 with PDB 2NNQ"
From Rizzo_Lab
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Inside the fraglib directory create a new input file for fragment generation. | Inside the fraglib directory create a new input file for fragment generation. | ||
| + | touch fraglib.in | ||
| + | |||
| + | Generate the fragments by calling the input file through DOCK6 | ||
| + | dock6 -i fraglib.in | ||
| + | |||
| + | Answer the prompted questions interactively using the following lines. | ||
| + | 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 yes | ||
| + | internal_energy_rep_exp 12 | ||
| + | internal_energy_cutoff 100.0 | ||
| + | ligand_atom_file /Path_to_file/2nnq_lig_withH.mol2 | ||
| + | limit_max_ligands no | ||
| + | skip_molecule no | ||
| + | read_mol_solvation no | ||
| + | calculate_rmsd no | ||
| + | use_database_filter no | ||
| + | orient_ligand yes | ||
| + | automated_matching yes | ||
| + | receptor_site_file /Path_to_file/selected_spheres.sph | ||
| + | max_orientations 1000 | ||
| + | critical_points no | ||
| + | chemical_matching no | ||
| + | use_ligand_spheres no | ||
| + | bump_filter no | ||
| + | score_molecules no | ||
| + | atom_model all | ||
| + | vdw_defn_file /gpfs/projects/AMS536/zzz.programs/dock6/parameters/vdw_AMBER_parm99.defn | ||
| + | flex_defn_file /gpfs/projects/AMS536/zzz.programs/dock6/parameters/flex.defn | ||
| + | flex_drive_file /gpfs/projects/AMS536/zzz.programs/dock6/parameters/flex_drive.tbl | ||
| + | ligand_outfile_prefix output | ||
| + | write_orientations no | ||
| + | num_scored_conformers 1 | ||
| + | rank_ligands no | ||
==Focused Denovo Growth== | ==Focused Denovo Growth== | ||
Revision as of 12:15, 27 February 2018
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.
touch fraglib.in
Generate the fragments by calling the input file through DOCK6
dock6 -i fraglib.in
Answer the prompted questions interactively using the following lines.
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 yes internal_energy_rep_exp 12 internal_energy_cutoff 100.0 ligand_atom_file /Path_to_file/2nnq_lig_withH.mol2 limit_max_ligands no skip_molecule no read_mol_solvation no calculate_rmsd no use_database_filter no orient_ligand yes automated_matching yes receptor_site_file /Path_to_file/selected_spheres.sph max_orientations 1000 critical_points no chemical_matching no use_ligand_spheres no bump_filter no score_molecules no atom_model all vdw_defn_file /gpfs/projects/AMS536/zzz.programs/dock6/parameters/vdw_AMBER_parm99.defn flex_defn_file /gpfs/projects/AMS536/zzz.programs/dock6/parameters/flex.defn flex_drive_file /gpfs/projects/AMS536/zzz.programs/dock6/parameters/flex_drive.tbl ligand_outfile_prefix output write_orientations no num_scored_conformers 1 rank_ligands no
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
