DOCK GA Tutorials

For this experiment required files will include 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