Difference between revisions of "DOCK GA Tutorials"

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For this experiment required files will include
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*[[2019 DOCK GA tutorial 1 with 2NNQ]]
2NNQ.lig.mol2
 
=='''I. Fragment Library Generation for 2NNQ'''==
 
 
 
===Fragment Libraries===
 
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.
 
 
 
The first step for this experiment is to generate a directory to perform the work in
 
      mkdir 2NNQ_GA
 
Go into this new directory and then create another directory that will store all the fragment molecules
 
      mkdir fraglib
 
Enter the file directory fraglib
 
      cd fraglib
 
Create a new file called 2NNQ.fraglib
 
      touch 2NNQ.fraglib
 
      dock6 -i 2NNQ.fraglib
 
Answer the following prompts using these responses
 
    conformer_search_type                                        flex
 
    write_fragment_libraries                                    yes
 
    fragment_library_prefix                                      2NNQ.fraglib
 
    fragment_library_freq_cutoff                                1
 
    fragment_library_sort_method                                freq
 
    fragment_library_trans_origin                                no
 
    use_internal_energy                                          no
 
    ligand_atom_file                                            ../../2NNQ_Tutorial/1.dockprep/2nnq_lig_withH.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
 
    atom_model                                                  all
 
    vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6/parameters/vdw_AMBER_parm99.defn
 
    flex_defn_file                                              /gpfs/projects/AMS536/zzz.programs/dock6/parameters/flex.defn
 
    flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6/parameters/flex_drive.tbl
 
    ligand_outfile_prefix                                        2NNQ_frag_output
 
    write_orientations                                          no
 
    num_scored_conformers                                        1
 
    rank_ligands                                                no
 
 
 
The only aspect that is relevant of this fragment library generated is the torsion environment that should be titled 2NNQ.fraglib_torenv.dat
 
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
 
    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
 
 
 
This should generate a new list of torsion environments titled unique_full_sorted_fraglib.dat
 
=='''II. Performing a GA using 2NNQ'''==
 
 
 
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.
 
    mkdir 2NNQ_GA_results
 
    cd 2NNQ_GA_results
 
    touch 2NNQ_GA.in
 
Following this dock6 will be performed on the molecule
 
    dock6 -i 2NNQ_GA.in -o 2NNQ_GA.out
 
Input the following in order to get the GA working properly
 

Latest revision as of 16:29, 24 June 2019