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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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| − | The only aspect that is relevant of this fragment library generated is the torsion environment that should be titled 2NNQ.fraglib_torenv.dat
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| − | Following this step the torsion environments of this molecule will be combined with the file titled full_sorted_fraglib.dat using the python software combine_torenv.py
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| − | py /gpfs/projects/rizzo/zzz.programs/torsion_env_combination/combine_torenv.py 2NNQ.fraglib_torenv.dat /gpfs/projects/rizzo/zzz.programs/dock6.10_2019.06.18/parameters/fraglib_torenv.dat
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| − | This should generate a new list of torsion environments titled unique_full_sorted_fraglib.dat
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| − | =='''II. Performing a GA using 2NNQ'''==
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| − | For this part a new directory will be created in the 2NNQ_GA. This will just be 2NNQ_GA_results. cd into that directory and create a new file titled 2NNQ_GA.in.
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| − | mkdir 2NNQ_GA_results
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| − | cd 2NNQ_GA_results
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| − | touch 2NNQ_GA.in
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| − | Following this dock6 will be performed on the molecule
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| − | dock6 -i 2NNQ_GA.in -o 2NNQ_GA.out
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| − | Input the following in order to get the GA working properly
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