Difference between revisions of "2020 Denovo tutorial 3 with PDBID 4F4P"
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==Fragment Librarie== | ==Fragment Librarie== | ||
| + | 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. | ||
| + | vi fraglib.in | ||
| + | |||
| + | Generate the fragments by calling the input file through DOCK6 | ||
| + | dock6 -i fraglib.in -o fradlib.out | ||
| + | |||
| + | 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 9 | ||
| + | internal_energy_cutoff 100.0 | ||
| + | ligand_atom_file (your path for VS docking)/001.files/4f4p_lig_h.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 (your path for VS docking)/002.surface_spheres/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/dock6.9_release/parameters/vdw_AMBER_parm99.defn | ||
| + | flex_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex.defn | ||
| + | flex_drive_file /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex_drive.tbl | ||
| + | ligand_outfile_prefix output | ||
| + | write_orientations no | ||
| + | num_scored_conformers 1 | ||
| + | rank_ligands no | ||
Revision as of 10:32, 10 March 2020
I. Focused De Novo Design with PDB 4F4P
This tutorial assumes that you have finished the virtual screening of this system ([1]). We are going to used some of the files generated by the VS toturial.
Fragment Librarie
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.
vi fraglib.in
Generate the fragments by calling the input file through DOCK6
dock6 -i fraglib.in -o fradlib.out
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 9 internal_energy_cutoff 100.0 ligand_atom_file (your path for VS docking)/001.files/4f4p_lig_h.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 (your path for VS docking)/002.surface_spheres/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/dock6.9_release/parameters/vdw_AMBER_parm99.defn flex_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex.defn flex_drive_file /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex_drive.tbl ligand_outfile_prefix output write_orientations no num_scored_conformers 1 rank_ligands no
