Difference between revisions of "Fragment Library Generation"
From Rizzo_Lab
Stonybrook (talk | contribs) (Created page with "An example of an input file to generate a fragment library calling DOCK6: conformer_search_type flex user_specified_anchor ...") |
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write_growth_tree no | write_growth_tree no | ||
write_fragment_libraries yes | write_fragment_libraries yes | ||
| − | fragment_library_prefix | + | fragment_library_prefix fraglib |
| − | fragment_library_freq_cutoff | + | fragment_library_freq_cutoff 10 |
fragment_library_sort_method ${SORT_METHOD} | fragment_library_sort_method ${SORT_METHOD} | ||
fragment_library_trans_origin no | fragment_library_trans_origin no | ||
use_internal_energy no | use_internal_energy no | ||
| − | ligand_atom_file | + | ligand_atom_file /PATH/001.files/compound_library.mol2 |
limit_max_ligands no | limit_max_ligands no | ||
skip_molecule no | skip_molecule no | ||
| Line 29: | Line 29: | ||
minimize_ligand no | minimize_ligand no | ||
atom_model all | atom_model all | ||
| − | vdw_defn_file | + | vdw_defn_file /PATH/001.files/vdw.defn |
| − | flex_defn_file | + | flex_defn_file /PATH/001.files/flex.defn |
| − | flex_drive_file | + | flex_drive_file /PATH/001.files/flex_drive.tbl |
ligand_outfile_prefix output | ligand_outfile_prefix output | ||
write_orientations no | write_orientations no | ||
num_scored_conformers 1 | num_scored_conformers 1 | ||
rank_ligands no | rank_ligands no | ||
Revision as of 16:07, 15 June 2017
An example of an input file to generate a fragment library calling DOCK6:
conformer_search_type flex
user_specified_anchor no
limit_max_anchors no
min_anchor_size 5
pruning_use_clustering no
pruning_max_orients 100
pruning_orient_score_cutoff 100.0
pruning_max_conformers 75
pruning_conformer_score_cutoff 100.0
use_clash_overlap no
write_growth_tree no
write_fragment_libraries yes
fragment_library_prefix fraglib
fragment_library_freq_cutoff 10
fragment_library_sort_method ${SORT_METHOD}
fragment_library_trans_origin no
use_internal_energy no
ligand_atom_file /PATH/001.files/compound_library.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
minimize_ligand no
atom_model all
vdw_defn_file /PATH/001.files/vdw.defn
flex_defn_file /PATH/001.files/flex.defn
flex_drive_file /PATH/001.files/flex_drive.tbl
ligand_outfile_prefix output
write_orientations no
num_scored_conformers 1
rank_ligands no
