View source for 2017 Denovo design tutorial 2 with PDB 4QMZ

==2017 Denovo design tutorial 2 with PDB 4QMZ==

The Denovo module of DOCK is a relatively new feature as of Fall 2016 that constructs new ligand molecules inside a protein active site from a library of user-specified "fragments." These novel ligand molecules are scored based on a number of unique scoring algorithms/criteria specified. The fragments used are common chemical functional groups -- or building blocks -- that are typically selected from a ZINC library of millions of compounds based off of their frequency of appearance. These fragments are classified as scaffolds, linkers, or side chains, according to the number of atomic positions that are permitted to seed growth: 3, 2, and 1 atoms, respectively. Thus, a scaffold could seed growth from three different atoms, having three linkers bonded to each position, and a linker could seed growth on two positions, and a side-chain on one position.
Once the molecules are built within the active site, their interactions with the protein are scored using the user-specified method of scoring. This tutorial will walk through the steps needed to run a Denovo calculation on the 4QMZ system from the 2017 DOCK tutorial. This method will utilize the multi-grid scoring function, called through the descriptor score. Ensure you have all the folders and files necessary from running the 2017 tutorial. Users are encouraged to run through the traditional DOCK tutorial for the 4qmz system as many of the files are recycled for the denovo experiments.
Before running the calculation, it's worth looking through the "Things to Keep in Mind" section at the bottom for some good pieces of information.

==Additional Files Needed==

To run the Denovo code with multigrid scoring you need these files:
     fraglib_scaffold.mol2                                                  <-- LIRed
     fraglib_linker.mol2                                                    <-- LIRed
     fraglib_sidechain.mol2                                                 <-- LIRed
     anchor_library.mol2                                                    <--LIRed
     fraglib_torenv.dat                                                     <-- LIRed
     selected_spheres.sph                                                   <-- make your own
     primary_residues_multigrid.bmp / .nrg                                  <-- make your own
     multigrid_minimized_ligand.mol2                                        <-- make your own
     vdw_AMBER_parm99.defn                                                  <--needed for regular dock
     flex.defn                                                              <--needed for regular dock
     flex_drive.tbl                                                         <-- needed for regular dock
     vdw_DumHyd.defn (needed for scoring functions other than multigrid)    <-- LIRed 
The fragment libraries and parameter files must be obtained prior to the Denovo calculation, and can be found on LIRed through the paths:
   /gpfs/home/guest43/scratch/denovo/trial_denovo/000.fraglib 

   /trial_denovo/zzz.parameters/
Everything else is generated through this tutorial, prior to running the Denovo code.


==Preparing The Files==
Before running Denovo on 4QMZ, please ensure you have gone through the DOCK 2017 tutorial and have all the resulting files. The tutorial can be accessed through here.
You should have these files in your directory:
     4qmz.pdb
     4qmz.lig.mol2
     4qmz.rec.clean.mol2
     4qmz.rec.noH.mol2
     selected_spheres.sph
Additionally, you will also need these parameter files:
     vdw_AMBER_parm99.defn
     flex.defn
     flex_drive.tbl
In order to run Denovo with multigrid scoring, we must first go through several steps:
 1). Create a primary residue text file and a reference text file -- selects the primary residues of interest.

 2). Make a multigrid file for each specified residue -- forms a grid for each residue specified in previous step.

 3). Minimizes ligand mol2 file using multigrids from previous step.

 4). Rescores ligand on multigrid to yield a minimized ligand .mol2 file. This serves as the reference ligand for Denovo calculations.

Luckily, our good friend Brian generated some extremely robust scripts to make this process easier. There is one script for each step, but we will only use the simple input files for DOCK. If you are interested in using the scripts (and a lot of debugging), they can be found on lired under: /gfps/home/guest43/scratch/denovo/trial_denovo/run/ .

==Dock Specifying Primary Residues==
Create a directory within your working directory titled 008.footprint_rescore. This is where all pertinent files from this step will go, and where we will run our calculation from.
The input file for this step should be titled 4qmz.footprint_rescore.in, and should look like (substitute your own directory path ~/your/own/directory/01.dockprep/4qmz.lig.mol2) :

   conformer_search_type                                        rigid
   use_internal_energy                                          no
   ligand_atom_file                                             /gpfs/home/stelehany/rizzo_rot_research/dock_tutorial/01.dockprep/4qmz.lig.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                                              yes
   contact_score_primary                                        no
   contact_score_secondary                                      no
   grid_score_primary                                           no
   grid_score_secondary                                         no
   multigrid_score_primary                                      no
   multigrid_score_secondary                                    no
   dock3.5_score_primary                                        no
   dock3.5_score_secondary                                      no
   continuous_score_primary                                     no
   continuous_score_secondary                                   no
   footprint_similarity_score_primary                           yes
   footprint_similarity_score_secondary                         no
   fps_score_use_footprint_reference_mol2                       yes
   fps_score_footprint_reference_mol2_filename                  /gpfs/home/stelehany/rizzo_rot_research/dock_tutorial/01.dockprep/4qmz.lig.mol2
   fps_score_foot_compare_type                                  Euclidean
   fps_score_normalize_foot                                     no
   fps_score_foot_comp_all_residue                              no
   fps_score_choose_foot_range_type                             threshold
   fps_score_vdw_threshold                                      1
   fps_score_es_threshold                                       0.5
   fps_score_hb_threshold                                       0.5
   fps_score_use_remainder                                      yes
   fps_score_receptor_filename                                  /gpfs/home/stelehany/rizzo_rot_research/dock_tutorial/01.dockprep/4qmz.rec.mol2
   fps_score_vdw_att_exp                                        6
   fps_score_vdw_rep_exp                                        12
   fps_score_vdw_rep_rad_scale                                  1
   fps_score_use_distance_dependent_dielectric                  yes
   fps_score_dielectric                                         4.0
   fps_score_vdw_fp_scale                                       1
   fps_score_es_fp_scale                                        1
   fps_score_hb_fp_scale                                        0
   pharmacophore_score_secondary                                no
   descriptor_score_secondary                                   no
   gbsa_zou_score_secondary                                     no
   gbsa_hawkins_score_secondary                                 no
   SASA_score_secondary                                         no
   amber_score_secondary                                        no
   minimize_ligand                                              no
   atom_model                                                   all
   vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dn_dock.6.7/parameters/vdw_AMBER_parm99.defn
   flex_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dn_dock.6.7/parameters/flex.defn
   flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dn_dock.6.7/parameters/flex_drive.tbl
   ligand_outfile_prefix                                        output
   write_footprints                                             yes
   write_hbonds                                                 no
   write_orientations                                           no
   num_scored_conformers                                        1
   rank_ligands                                                 no

This calculation should be very quick (~10 seconds) and result in three output files:
 4qmz.footprint_rescore.out 
 output_footprint_scored.txt
 output_scored.mol2


Now, we must declare the primary residues in the active site and generate a grid file for each. Create a new file in the text editor named 4qmz.primary_residues.sh and write this inside of it (copied from Brian's script *.fpsrescore.qsub.sh):

   #!/bin/bash 
   grep -A 1 "range_union" footprintrescore.out |
   grep -v "range_union" |
   grep -v "\-" |
   sed -e '{s/,/\n/g}' |
   sed -e '{s/ //g}' |
   sed '/^$/d' |
   sort -n |
   uniq > temp.dat
   for i in `cat temp.dat`; do printf "%0*d\n" 3 $i; done > 4qmz.primary_residues.dat
   for RES in `cat temp.dat`
   do
           grep " ${RES} " output_footprint_scored.txt  |
           awk -v temp=${RES} '{if ($2 == temp) print $0;}' |
           awk '{print $1 "  " $3 "  " $4}' >> reference.txt
   done
   grep "remainder" output_footprint_scored.txt |
   sed -e '{s/,/  /g}' |
   tr -d '\n' |
   awk '{print $2 "  " $3 "  " $6}' >> reference.txt
   mv reference.txt 4qmz.reference.txt
   rm temp.dat

Run the script and you should have two new files:
 4qmz.primary_residues.dat
 4qmz.reference.txt 
These are our primary residues! Now we need to generate a grid for each one.


==Generating the Grids==

We must now generate a grid file for each residue. To do so, we will need the aid of another one of Brian's scripts: 4qmz.make_multigrids.qsub.sh. But before we can use his script, we need to generate two input files for Dock which will be called upon by the script. Create a file named 4qmz.multigrid.in inside your 007.multigrid folder with the following inside it:

   compute_grids                  yes
   grid_spacing                   0.4
   output_molecule                yes
   contact_score                  no
   chemical_score                 no
   energy_score                   yes
   energy_cutoff_distance         9999
   atom_model                     a
   attractive_exponent            6
   repulsive_exponent             9
   distance_dielectric            yes
   dielectric_factor              4
   bump_filter                    yes
   bump_overlap                   0.75
   receptor_file                  temp.mol2
   box_file                       ../03.box-grid/4qmz.box.pdb
   vdw_definition_file            /gpfs/projects/AMS536/zzz.programs/dn_dock.6.7/parameters/vdw_AMBER_parm99.defn
   chemical_definition_file       /gpfs/projects/AMS536/zzz.programs/dn_dock.6.7/parameters/chem.defn
   score_grid_prefix              temp.rec
   receptor_out_file              temp.rec.grid.mol2

Additionally, create a file named 4qmz.reference_multigrid.in:

 conformer_search_type                                        rigid 
 use_internal_energy                                          yes
 internal_energy_rep_exp                                      12
 internal_energy_cutoff                                       100.0
 ligand_atom_file                                             /gpfs/home/stelehany/rizzo_rot_research/dock_tutorial/01.dockprep/4qmz.lig.mol2
 limit_max_ligands                                            no
 skip_molecule                                                no
 read_mol_solvation                                           no
 calculate_rmsd                                               yes
 use_rmsd_reference_mol                                       yes
 rmsd_reference_filename                                      /gpfs/home/stelehany/rizzo_rot_research/dock_tutorial/01.dockprep/4qmz.lig.mol2
 use_database_filter                                          no
 orient_ligand                                                no
 bump_filter                                                  no
 score_molecules                                              yes
 contact_score_primary                                        no
 contact_score_secondary                                      no
 grid_score_primary                                           no
 grid_score_secondary                                         no
 multigrid_score_primary                                      yes
 multigrid_score_secondary                                    no
 multigrid_score_rep_rad_scale                                1
 multigrid_score_vdw_scale                                    1
 multigrid_score_es_scale                                     1
 multigrid_score_number_of_grids                              19
 multigrid_score_grid_prefix0                                 ../10.multigrid/4qmz.resid_017
 multigrid_score_grid_prefix1                                 ../10.multigrid/4qmz.resid_018
 multigrid_score_grid_prefix2                                 ../10.multigrid/4qmz.resid_019
 multigrid_score_grid_prefix3                                 ../10.multigrid/4qmz.resid_026
 multigrid_score_grid_prefix4                                 ../10.multigrid/4qmz.resid_039
 multigrid_score_grid_prefix5                                 ../10.multigrid/4qmz.resid_071
 multigrid_score_grid_prefix6                                 ../10.multigrid/4qmz.resid_087
 multigrid_score_grid_prefix7                                 ../10.multigrid/4qmz.resid_088
 multigrid_score_grid_prefix8                                 ../10.multigrid/4qmz.resid_089
 multigrid_score_grid_prefix9                                 ../10.multigrid/4qmz.resid_090
 multigrid_score_grid_prefix10                                ../10.multigrid/4qmz.resid_091
 multigrid_score_grid_prefix11                                ../10.multigrid/4qmz.resid_093
 multigrid_score_grid_prefix12                                ../10.multigrid/4qmz.resid_097
 multigrid_score_grid_prefix13                                ../10.multigrid/4qmz.resid_100
 multigrid_score_grid_prefix14                                ../10.multigrid/4qmz.resid_139
 multigrid_score_grid_prefix15                                ../10.multigrid/4qmz.resid_279
 multigrid_score_grid_prefix16                                ../10.multigrid/4qmz.resid_280
 multigrid_score_grid_prefix17                                ../10.multigrid/4qmz.resid_283
 multigrid_score_grid_prefix18                                /gpfs/home/stelehany/rizzo_rot_research/dock_tutorial/10.multigrid/4qmz.resid_remaining
 multigrid_score_fp_ref_mol                                   no
 multigrid_score_fp_ref_text                                  yes
 multigrid_score_footprint_text                               /gpfs/home/stelehany/rizzo_rot_research/dock_tutorial/09.footprint_rescore/4qmz.reference.txt
 multigrid_score_use_euc                                      yes
 multigrid_score_use_norm_euc                                 no
 multigrid_score_use_cor                                      no
 multigrid_vdw_euc_scale                                      1
 multigrid_es_euc_scale                                       1
 dock3.5_score_secondary                                      no
 continuous_score_secondary                                   no
 footprint_similarity_score_secondary                         no
 ph4_score_secondary                                          no
 descriptor_score_secondary                                   no
 gbsa_zou_score_secondary                                     no
 gbsa_hawkins_score_secondary                                 no
 SASA_descriptor_score_secondary                              no
 amber_score_secondary                                        no
 minimize_ligand                                              yes
 simplex_max_iterations                                       1000
 simplex_tors_premin_iterations                               0
 simplex_max_cycles                                           1
 simplex_score_converge                                       0.1
 simplex_cycle_converge                                       1.0
 simplex_trans_step                                           1.0
 simplex_rot_step                                             0.1
 simplex_tors_step                                            10.0
 simplex_random_seed                                          0
 simplex_restraint_min                                        yes
 simplex_coefficient_restraint                                5.0
 atom_model                                                   all
 vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dn_dock.6.7/parameters/vdw_AMBER_parm99.defn
 flex_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dn_dock.6.7/parameters/flex.defn
 flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dn_dock.6.7/parameters/flex_drive.tbl
 ligand_outfile_prefix                                        output
 write_orientations                                           no
 num_scored_conformers                                        1
 rank_ligands                                                 no

Now that we have our input files, we can form the script that will call upon them to generate the grid files for each specified residue. Create a blank file named 4qmz.make_multigrids.qsub.sh in your 007.multigrid folder. Then transcribe into it:

 cd /gpfs/home/stelehany/rizzo_rot_research/dock_tutorial/09.footprint_rescore
 export PRIMARY_RES=` cat 4qmz.primary_residues.dat | sed -e 's/\n/ /g' `
 export DOCKHOME="/gpfs/projects/AMS536/zzz.programs/dn_dock.6.7/"
 python /gpfs/projects/AMS536/zzz.programs/dn_dock.6.7/bin/multigrid_fp_gen.py 4qmz.rec.mol2 4qmz.resid 4qmz.multigrid.in ${PRIMARY_RES}
 rm temp.mol2
 rm 4qmz.resid_*.rec.grid.mol2
 /gpfs/projects/AMS536/zzz.programs/dn_dock.6.7/bin/dock6.dn -i 4qmz.reference_multigridmin.in -o 4qmz.reference_multigridmin.out
 mv output_scored.mol2 4qmz.lig.multigridmin.mol2
 cp 4qmz.lig.multigridmin.mol2 ../10.multigrid

Change the path to Dock and your primary residue file if necessary, and ensure you are using a version of Dock with the Denovo code. If you get an error that says something like "cannot stat *.nrg / *.bmp" etc, check to make sure your directories are all pointing to the right places in your two input files. After running this script, you should be given a plethora of different files. If you are running on the 4qmz system, you should have 19 different residues: 18 individual residues, and a 19th file containing the grid for the rest of the residues. You will have four files for each residue: a .bmp file, a .mol2 file, a .nrg file, and a .out file (for each residue!). Additionally you should have two other files: 4qmz.lig.multigridmin.mol2, 4qmz.reference_multigridmin.out. Check your output file for any errors and to make sure everything ran to completion. Visualize your ligand in Chimera to make sure it contains atoms and looks like a real chemical structure. You should have something that looks like this:

  [[File:4qmz multigrid min.png]]

In addition to ensuring the ligand still seems reasonable, it may be worthwhile and interesting to visualize the ligand with the primary residues to create a distilled down active site like this (ligand is highlighted green for ease of visualization):

 [[File:4qmz w prim res.png]]

 [[File:4qmz w prim res2.png]]

 [[File:4qmz w prim res3.png]]

 [[File:4qmz w prim res4.png]]

==Minimizing Ligand on the Grids==

We're taking the input here straight from Brian's script for this part (run.003e.mg_rescore.sh). Create an input file named 4qmz.parents_multigridmin.in with this inside it:

 conformer_search_type                                        rigid
 use_internal_energy                                          yes
 internal_energy_rep_exp                                      12
 internal_energy_cutoff                                       100.0
 ligand_atom_file                                             /gpfs/home/stelehany/rizzo_rot_research/dock_tutorial/01.dockprep/4qmz.lig.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                                              yes
 contact_score_primary                                        no
 contact_score_secondary                                      no
 grid_score_primary                                           no
 grid_score_secondary                                         no
 multigrid_score_primary                                      yes
 multigrid_score_secondary                                    no
 multigrid_score_rep_rad_scale                                1
 multigrid_score_vdw_scale                                    1
 multigrid_score_es_scale                                     1
 multigrid_score_number_of_grids                              19
 multigrid_score_grid_prefix0                                 4qmz.resid_017
 multigrid_score_grid_prefix1                                 4qmz.resid_018
 multigrid_score_grid_prefix2                                 4qmz.resid_019
 multigrid_score_grid_prefix3                                 4qmz.resid_026
 multigrid_score_grid_prefix4                                 4qmz.resid_039
 multigrid_score_grid_prefix5                                 4qmz.resid_071
 multigrid_score_grid_prefix6                                 4qmz.resid_087
 multigrid_score_grid_prefix7                                 4qmz.resid_088
 multigrid_score_grid_prefix8                                 4qmz.resid_089
 multigrid_score_grid_prefix9                                 4qmz.resid_090
 multigrid_score_grid_prefix10                                4qmz.resid_091
 multigrid_score_grid_prefix11                                4qmz.resid_093
 multigrid_score_grid_prefix12                                4qmz.resid_097
 multigrid_score_grid_prefix13                                4qmz.resid_100
 multigrid_score_grid_prefix14                                4qmz.resid_139
 multigrid_score_grid_prefix15                                4qmz.resid_279
 multigrid_score_grid_prefix16                                4qmz.resid_280
 multigrid_score_grid_prefix17                                4qmz.resid_283
 multigrid_score_grid_prefix18                                4qmz.resid_remaining
 multigrid_score_fp_ref_mol                                   no
 multigrid_score_fp_ref_text                                  yes
 multigrid_score_footprint_text                               4qmz.reference.txt
 multigrid_score_foot_compare_type                            Euclidean
 multigrid_score_normalize_foot                               no
 multigrid_score_vdw_euc_scale                                1.0
 multigrid_score_es_euc_scale                                 1.0
 dock3.5_score_secondary                                      no
 continuous_score_secondary                                   no
 footprint_similarity_score_secondary                         no
 pharmacophore_score_secondary                                no
 descriptor_score_secondary                                   no
 gbsa_zou_score_secondary                                     no
 gbsa_hawkins_score_secondary                                 no
 SASA_score_secondary                                         no
 amber_score_secondary                                        no
 minimize_ligand                                              yes
 simplex_max_iterations                                       1000
 simplex_tors_premin_iterations                               0
 simplex_max_cycles                                           1
 simplex_score_converge                                       0.1
 simplex_cycle_converge                                       1.0
 simplex_trans_step                                           1.0
 simplex_rot_step                                             0.1
 simplex_tors_step                                            10.0
 simplex_random_seed                                          0
 simplex_restraint_min                                        yes
 simplex_coefficient_restraint                                5.0
 atom_model                                                   all
 vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dn_dock.6.7/parameters/vdw_AMBER_parm99.defn
 flex_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dn_dock.6.7/parameters/flex.defn
 flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dn_dock.6.7/parameters/flex_drive.tbl
 ligand_outfile_prefix                                        output
 write_footprints                                             no
 write_orientations                                           no
 num_scored_conformers                                        1
 rank_ligands                                                 no

After running this with dock6 you should have an output file (which should be checked for errors, as always) and a .mol2 file named output_scored.mol2. Rename this to 4qmz.parents_multigridmin.mol2, and visualize it in Chimera, to ensure you still have a realistic molecule. This is the mol2 file of the ligand minimized using the multigrid scoring. This will serve as our reference molecule for guided growth!

==Running Denovo==

===Creating the Input File===

===Creating a script to submit to Seawulf===

===Viewing the Results===

==Things to Keep in Mind==

===Length of Denovo Calculations===