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| − | For this experiment required files will include
| + | *[[2024 DOCK GA tutorial 1 with 1NDV]] |
| − | 2NNQ.lig.mol2
| + | *[[2019 DOCK GA tutorial 1 with 2NNQ]] |
| − | =='''I. Fragment Library Generation for 2NNQ'''==
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| − | | |
| − | ===Fragment Libraries===
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| − | For this experiment a general fragment library to account for all the possible ligands the GA can produce. A focused Fragment library will not be enough to account for all the possibilities since it is too small of a set of data.
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| − | The first step for this experiment is to generate a directory to perform the work in
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| − | mkdir 2NNQ_GA
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| − | Go into this new directory and then create another directory that will store all the fragment molecules
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| − | mkdir fraglib
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| − | Enter the file directory fraglib
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| − | cd fraglib
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| − | Create a new file called 2NNQ.fraglib
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| − | touch 2NNQ.fraglib
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| − | dock6 -i 2NNQ.fraglib
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| − | Answer the following prompts using these responses
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| − | conformer_search_type flex
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| − | write_fragment_libraries yes
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| − | fragment_library_prefix 2NNQ.fraglib
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| − | fragment_library_freq_cutoff 1
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| − | fragment_library_sort_method freq
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| − | fragment_library_trans_origin no
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| − | use_internal_energy no
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| − | ligand_atom_file ../../2NNQ_Tutorial/1.dockprep/2nnq_lig_withH.mol2
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| − | limit_max_ligands no
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| − | skip_molecule no
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| − | read_mol_solvation no
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| − | calculate_rmsd no
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| − | use_database_filter no
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| − | orient_ligand no
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| − | bump_filter no
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| − | score_molecules no
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| − | atom_model all
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| − | vdw_defn_file /gpfs/projects/AMS536/zzz.programs/dock6/parameters/vdw_AMBER_parm99.defn
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| − | flex_defn_file /gpfs/projects/AMS536/zzz.programs/dock6/parameters/flex.defn
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| − | flex_drive_file /gpfs/projects/AMS536/zzz.programs/dock6/parameters/flex_drive.tbl
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| − | ligand_outfile_prefix 2NNQ_frag_output
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| − | write_orientations no
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| − | num_scored_conformers 1
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| − | rank_ligands no
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