docking.wic

docking/autodock-vina/docking.wic

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+inputs:
+  sdf_path:
+    type: File
+    format:
+    - edam:format_3814
+
+steps:
+# Ligand
+# NOTE: Searching for conformers tends to cause the ligand to curl up into a ball.
+# Although this lowers its energy in isolation, the decreased surface area tends
+# to weaken the binding free energy! (as reported by autodock vina)
+    flc.wic:
+      in:
+        sdf_path: sdf_path
+#    minimize_ligand_only.wic:
+
+# NOTE: We converted to mol2 format above because it allows explicit charges.
+# Thus, if we only infer charges once and then preserve them, we don't have to
+# worry about using different charges in autodock vs molecular dynamics.
+# It also stores explicit bond order info, so the topology will be identical.
+# (Also note that we did NOT convert to pdb and then to pdbqt, because that loses both!)
+
+# NOTE: Rename all residues to MOL before calling acpypye. Otherwise, acpype crashes with:
+# "ERROR: more than one residue detected '{'UNL', 'MOL'}'"
+    python3_mol2_to_mol2:
+      in:
+        script: !ii /rename_residues_mol.py # NOTE: Initial / required
+        input_mol2_path: !* ligand_min.mol2
+      out:
+      - output_mol2_path: !& conformer.mol2
+
+# NOTE: minimize before calling acpype so 1. tleap complains less about close contacts:
+# /usr/local/bin/teLeap: Warning!
+# Close contact of 1.418311 angstroms between .R<UNL 1>.A<CG 8> and .R<UNL 1>.A<HD2 30>
+# and 2. acpype doesn't complain about 'ERROR: Atoms TOO alone (> 3.0 Ang.)'
+# (acpype suggests using --force, but it's better to just minimize.)
+    acpype:
+    # NOTE: We are using our own acpypye CWL adapter (NOT the biobb version) so
+    # we have the choice of using charges from the mol2 file.
+      in:
+        input_path: !* conformer.mol2 # Do NOT use pose_ligand.pdb
+      out:
+      - output_itp_path: !& ligand_GMX.itp
+        # NOTE: Although we don't need the *.itp topology file yet, we
+        # need to use these coordinates with autodock because they are
+        # sorted to agree with the *.itp topology include file.
+        # Otherwise, we will get the grompp atom name warning (see below).
+      - output_gro_path: !& ligand_GMX.gro
+      - output_top_path: !& ligand_GMX.top
+        #charge_method: user # take charges from mol2 file
+# NOTE: acpype doesn't add forcefield or water topology #include lines.
+    bash_top:
+      in:
+        script: !ii /gmx_add_topology_includes.sh # NOTE: Initial / required
+        input_top_path: !* ligand_GMX.top
+      out:
+      - output_top_path: !& ligand_GMX_includes.top
+    zip_top:
+      in:
+        input_top_path: !* ligand_GMX_includes.top
+        input_itp_path: !* ligand_GMX.itp
+      out:
+      - output_top_zip_path: !& ligand_GMX.zip
+
+# Docking
+    convert_ligand_mol2_to_pdbqt_obabel.wic:
+#    convert_ligand_mol2_to_pdbqt_mdanalysis.wic: # generates ligand_rigid.pdbqt only
+
+    autodock_vina_run:
+      in:
+        input_ligand_pdbqt_path: !* ligand_flex.pdbqt
+        #input_ligand_pdbqt_path: !* ligand_rigid.pdbqt
+        input_receptor_pdbqt_path: !* pdb.pdbqt
+        input_box_path: !* box.pdb
+      out:
+      - output_pdbqt_path: !& poses_ligand.pdbqt
+      - output_log_path: !& vina.log
+    extract_model_pdbqt:
+      in:
+        input_pdbqt_path: !* poses_ligand.pdbqt
+        output_pdbqt_path: !ii pose_ligand.pdbqt
+        config: !ii
+          model: 1 # NOTE: score, rmsd l.b., rmsd u.b. stored in REMARK lines
+      out:
+      - output_pdbqt_path: !& pose_ligand.pdbqt
+    convert_xyz:
+      in:
+        input_path: !* pose_ligand.pdbqt
+        output_xyz_path: !ii pose_ligand.xyz
+      out:
+      - output_xyz_path: !& pose_ligand.xyz
+# Molecular Dynamics combine receptor & ligand
+    append_ligand:
+      in:
+        input_itp_path: !* ligand_GMX.itp
+        input_top_zip_path: !* receptor.zip
+      out:
+      - output_top_zip_path: !& complex_vac.zip
+    combine_structure:
+      in:
+        input_structure1: !* receptor.xyz  # receptor_hydrogens.pdb
+        input_structure2: !* pose_ligand.xyz
+      out:
+      - output_structure_path: !& complex_vac.pdb
+
+wic:
+   graphviz:
+     label: Cheminformatics + Docking + Initial Topology Setup
+   steps:
+     (2, python3_mol2_to_mol2):
+       wic:
+         graphviz:
+           label: Rename Ligand\nResidues to MOL
+     (3, acpype):
+       wic:
+         graphviz:
+           label: Generate Ligand\nParameters & Topology
+     (4, bash_top):
+       wic:
+         graphviz:
+           label: Fix Gromacs\n Topology Includes
+     (5, zip_top):
+       wic:
+         graphviz:
+           label: Zip Topology/Files
+     (7, autodock_vina_run):
+       wic:
+         graphviz:
+           label: Perform Docking
+     (8, extract_model_pdbqt):
+       wic:
+         graphviz:
+           label: Extract Best\nDocking Pose
+     (9, convert_xyz):
+       wic:
+         graphviz:
+           label: Convert Complex\npdbqt to xyz
+     (10, append_ligand):
+       wic:
+         graphviz:
+           label: Append Ligand Topology\nto Receptor Topology
+     (11, combine_structure):
+       wic:
+         graphviz:
+           label: Append Ligand Coordinates\nto Receptor Coordinates

docking/autodock-vina/docking_stability.wic

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+inputs:
+  sdf_path:
+    type: File
+    format:
+    - edam:format_3814
+
+steps:
+  docking.wic:
+    in:
+      # NOTE: sdf_path is currently only necessary
+      # due to a limitation of the inlineing implementation.
+      sdf_path: sdf_path
+  stability.wic:
+    in:
+      # NOTE: crd_path and top_zip_path are currently only necessary
+      # due to a limitation of the inlineing implementation.
+      crd_path: !* complex_vac.pdb
+      top_zip_path: !* complex_vac.zip
+      nsteps: !ii 100000
+      dt: !ii 0.002
+      temperature: !ii 298.0
+      pressure: !ii 1.0
+wic:
+  graphviz:
+    label: Docking + MD Stability Analysis
+  steps:
+    (1, docking.wic):
+      wic:
+        inlineable: True
+    (2, stability.wic):
+      wic:
+        inlineable: False
+        steps:
+          (2, basic.wic):
+            wic:
+              steps:
+                (3, prod.wic):
+                  wic:
+                    steps:
+                      (4, cwl_subinterpreter_analysis.wic):
+                        wic:
+                          implementation: complex
+          (3, analysis.wic):
+            wic:
+              steps:
+                (1, analysis_realtime.wic):
+                  wic:
+                    implementation: complex