Difference between revisions of "2021 Denovo tutorial 3 with PDBID 1S19"
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===Fragment Libraries=== | ===Fragment Libraries=== | ||
| + | |||
| + | We will use a focused fragment library file based on the original ligand. To begin, we will create a new directory for this. | ||
| + | |||
| + | mkdir fraglib | ||
| + | |||
| + | Create a new file called '''fragment.in''' with the following inputs. | ||
| + | |||
| + | 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 ../001_dock/1s19_ligand_dockprep.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 ../02_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 fragment.out | ||
| + | write_orientations no | ||
| + | num_scored_conformers 1 | ||
| + | rank_ligands no | ||
| + | |||
| + | To run this, type: | ||
| + | |||
| + | dock6 -i fragment.in -o fragment.out | ||
===Focused Denovo Growth=== | ===Focused Denovo Growth=== | ||
Revision as of 15:12, 8 March 2021
This tutorial continues where we left off from the virtual screening of 1S19, a structure of the vitamin D nuclear receptor bound to the side chain analogue calcipotriol.
Contents
Focused Denovo Design with PDB 1S19
In this section, we will generate new ligand structures using a fragment library. It will require the use of some of the output files from the Virtual Screen tutorial (found here).
Fragment Libraries
We will use a focused fragment library file based on the original ligand. To begin, we will create a new directory for this.
mkdir fraglib
Create a new file called fragment.in with the following inputs.
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 ../001_dock/1s19_ligand_dockprep.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 ../02_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 fragment.out write_orientations no num_scored_conformers 1 rank_ligands no
To run this, type:
dock6 -i fragment.in -o fragment.out
