Fragment Library Generation
From Rizzo_Lab
Revision as of 17:07, 15 June 2017 by Stonybrook (talk | contribs)
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
