vacuum minimization

cwl_adapters/combine_structure.cwl

@@ -12,7 +12,7 @@ baseCommand: ['python', '/combine_structure.py']
 
 hints:
   DockerRequirement:
-    dockerPull: ndonyapour/combine_structure
+    dockerPull: ndonyapour/combine_structure_fix
 
 inputs:
   input_structure1:
@@ -40,6 +40,20 @@ inputs:
     - edam:format_3877 
     inputBinding:
       prefix: --input_structure2
+
+  input_top_zip_path:
+    label: Input zip file
+    doc: |-
+      Input zip file
+      Type: string
+      File type: input
+      Accepted formats: zip
+      Example file: https://github.com/bioexcel/biobb_md/blob/master/biobb_md/test/data/gromacs/genion.zip
+    type: File
+    format:
+    - edam:format_3987
+    inputBinding:
+      prefix: --input_top_zip_path
 
   output_structure_path:
     label: Output combined PDB file path

examples/docking/docking.yml

@@ -90,6 +90,7 @@ steps:
       in:
         input_structure1: '*receptor.xyz' # '*receptor_hydrogens.pdb'
         input_structure2: '*pose_ligand.xyz'
+        input_top_zip_path: '*complex_vac.zip'
         output_structure_path: '&complex_vac.pdb'
 
 wic:

examples/docking/dsb.yml

@@ -9,12 +9,16 @@ steps:
       sdf_path: ~sdf_path
 - stability.yml:
     in:
+      crd_path: '*complex_vac.pdb'
+      top_zip_path: '*complex_vac.zip'
       nsteps: 10000
       dt: 0.002
       temperature: 298.0
       pressure: 1.0
 - stability.yml:
     in:
+      crd_path: '*ligand_GMX.gro'
+      top_zip_path: '*ligand_GMX.zip'
       nsteps: 10000
       dt: 0.002
       temperature: 298.0
@@ -31,13 +35,18 @@ wic:
         environment:
           action: checkpoint
         steps:
-          (1, setup.yml):
+          (1, setup_vac_min.yml):
             wic:
               steps:
-                (4, genion):
-                  in:
-                    output_top_zip_path: '&genion_complex.zip'
+                (3, solv_ion.yml):
+                  wic:
+                    steps:
+                      (4, genion):
+                        in:
+                          output_top_zip_path: '&genion_complex.zip'
           (2, basic.yml):
+            in:
+              top_zip_path: '*genion_complex.zip'
             wic:
               steps:
                 (3, prod.yml):
@@ -72,13 +81,24 @@ wic:
           action: restore
           save_defs: ['genion_complex.zip', 'prod_complex.gro']
         steps:
-          (1, setup.yml):
+          (1, setup_vac_min.yml):
             wic:
               steps:
-                (4, genion):
-                  in:
-                    output_top_zip_path: '&genion_ligand.zip'
+                (1, topology.yml):
+                  wic:
+                    steps:
+                      (1, editconf):
+                        in: 
+                          output_crd_path: '&ligand_box.g96'
+                (3, solv_ion.yml):
+                  wic:
+                    steps:
+                      (4, genion):
+                        in:
+                          output_top_zip_path: '&genion_ligand.zip'
           (2, basic.yml):
+            in:
+              top_zip_path: '*genion_ligand.zip'
             wic:
               steps:
                 (3, prod.yml):

examples/docking/gen_topol_params.yml

@@ -65,6 +65,7 @@ steps:
     in:
       input_structure1: ~input_receptor_xyz_path
       input_structure2: '*pose_ligand.xyz'
+      input_top_zip_path: '*complex_vac.zip'
       output_structure_path: '&complex_vac.pdb'
 
 wic:

examples/docking/vs_demo_2.yml

@@ -128,13 +128,18 @@ wic:
       wic:
         inlineable: False # Due to yml wic tag inlineing issue and ~ inputs
         steps:
-          (1, setup.yml):
+          (1, setup_vac_min.yml):
             wic:
               steps:
-                (4, genion):
-                  in:
-                    output_top_zip_path: '&genion_complex.zip'
+                (3, solv_ion.yml):
+                  wic:
+                    steps:
+                      (4, genion):
+                        in:
+                          output_top_zip_path: '&genion_complex.zip'
           (2, basic.yml):
+            in:
+              top_zip_path: '*genion_complex.zip'
             wic:
               steps:
                 (3, prod.yml):

examples/docking/vs_demo_3.yml

@@ -106,13 +106,18 @@ wic:
       wic:
         inlineable: False # Due to yml wic tag inlineing issue and ~ inputs
         steps:
-          (1, setup.yml):
+          (1, setup_vac_min.yml):
             wic:
               steps:
-                (4, genion):
-                  in:
-                    output_top_zip_path: '&genion_complex.zip'
+                (3, solv_ion.yml):
+                  wic:
+                    steps:
+                      (4, genion):
+                        in:
+                          output_top_zip_path: '&genion_complex.zip'
           (2, basic.yml):
+            in:
+              top_zip_path: '*genion_complex.zip'
             wic:
               steps:
                 (3, prod.yml):

examples/docking/vs_demo_4.yml

@@ -135,13 +135,18 @@ wic:
       wic:
         inlineable: False # Due to yml wic tag inlineing issue and ~ inputs
         steps:
-          (1, setup.yml):
+          (1, setup_vac_min.yml):
             wic:
               steps:
-                (4, genion):
-                  in:
-                    output_top_zip_path: '&genion_complex.zip'
+                (3, solv_ion.yml):
+                  wic:
+                    steps:
+                      (4, genion):
+                        in:
+                          output_top_zip_path: '&genion_complex.zip'
           (2, basic.yml):
+            in:
+              top_zip_path: '*genion_complex.zip'
             wic:
               steps:
                 (3, prod.yml):

examples/gromacs/basic.yml

@@ -1,4 +1,8 @@
 inputs:
+  top_zip_path:
+    type: File
+    format:
+    - edam:format_3987
   nsteps:
     type: int
   dt:
@@ -16,6 +20,8 @@ steps:
 # to this level and use the following syntax to pass it to only one call site.
 # (Moreover, the former will create multiple definitions of &min.tpr, which is not allowed.)
   - min.yml:
+      in:
+        top_zip_path: ~top_zip_path
   - equil.yml:
   - prod.yml:
       in:

examples/gromacs/cg.yml

@@ -1,6 +1,13 @@
+inputs:
+  top_zip_path:
+    type: File
+    format:
+    - edam:format_3987
+
 steps:
   - grompp:
       in:
+        input_top_zip_path: ~top_zip_path
         config:
           mdp:
             integrator: cg

examples/gromacs/min.yml

@@ -1,9 +1,19 @@
+inputs:
+  top_zip_path:
+    type: File
+    format:
+    - edam:format_3987
+
 steps:
   - steep.yml:
+      in:
+        top_zip_path: ~top_zip_path
 # Fatal error:
 # The coordinates could not be constrained. Minimizer 'cg' can not handle
 # constraint failures, use minimizer 'steep' before using 'cg'.
   - cg.yml:
+      in:
+        top_zip_path: ~top_zip_path
 # Fatal error:
 # The combination of constraints and L-BFGS minimization is not implemented.
 # Either do not use constraints, or use another minimizer (e.g. steepest

examples/gromacs/setup_vac_min.yml

@@ -1,8 +1,37 @@
+inputs:
+  crd_path:
+    type: File
+    format:
+    - edam:format_1476
+    - edam:format_2033
+  top_zip_path:
+    type: File
+    format:
+    - edam:format_3987
+
 steps:
   - topology.yml:
+      in:
+        crd_path: ~crd_path
   - min.yml: # Minimize in vacuum first, then in solvent.
+      in:
+        top_zip_path: ~top_zip_path
   - solv_ion.yml:
-
+      in:
+        top_zip_path: ~top_zip_path
 wic:
   graphviz:
-    label: System Setup
+    label: System Setup
+  steps:
+    (1, topology.yml):
+      wic:
+        graphviz:
+          label: 'Initialize\nPeriodic Box'
+    (2, min.yml):
+      wic:
+        graphviz:
+          label: 'Vacuum Minimization'
+    (3, solv_ion.yml):
+      wic:
+        graphviz:
+          label: 'Add Water\nSolvent'

examples/gromacs/solv_ion.yml

@@ -1,12 +1,26 @@
+inputs:
+  top_zip_path:
+    type: File
+    format:
+    - edam:format_3987
+
 steps:
-  - editconf:
+#   - editconf:
+#       in:
+#         #input_crd_path: ~crd_path
+#         config:
+#           box_type: cubic
+#           distance_to_molecule: 1.2
+  - gmx_editconf:
       in:
-        config:
-          box_type: cubic
-          distance_to_molecule: 1.0
+        #input_crd_path: ~crd_path
+        #input_crd_path: '*complex_vac.pdb'
+        align_principal_axes: 0
+        box_type: cubic
+        distance_to_molecule: 1.2
   - solvate:
       in:
-        input_top_zip_path: '*complex_vac.zip'
+        input_top_zip_path: ~top_zip_path
         output_crd_path: '&solvate.gro'
         output_top_zip_path: '&solvate.zip'
   - grompp:
@@ -28,10 +42,10 @@ wic:
   graphviz:
     label: Solvation & Ionization
     ranksame:
-    - (1, editconf)
+    - (1, gmx_editconf)
     - (4, genion)
   steps:
-    (1, editconf):
+    (1, gmx_editconf):
       wic:
         graphviz:
           label: 'Initialize\nPeriodic Box'

examples/gromacs/stability.yml

@@ -18,12 +18,13 @@ inputs:
     - edam:format_3987
 
 steps:
-  - setup.yml:
+  - setup_vac_min.yml:
       in:
         crd_path: ~crd_path
         top_zip_path: ~top_zip_path
   - basic.yml:
       in:
+        top_zip_path: '*genion.zip'
         nsteps: ~nsteps
         dt: ~dt
         ref-t: ~temperature

examples/gromacs/steep.yml

@@ -1,10 +1,17 @@
+inputs:
+  top_zip_path:
+    type: File
+    format:
+    - edam:format_3987
+
 # On my machine, 10 iterations of steepest descent is sufficient to prevent
 # conjugate gradient from crashing. (i.e. pytest works for me!)
 # But using only 10 iterations is causing the tests on github actions to fail!
 # 25 seems to work, but let's just set it to 100.
 steps:
   - grompp:
       in:
+        input_top_zip_path: ~top_zip_path
         config:
           mdp:
             integrator: steep

examples/gromacs/topology.yml

@@ -1,10 +1,17 @@
+inputs:
+  crd_path:
+    type: File
+    format:
+    - edam:format_1476
+    - edam:format_2033
+
 steps:
 # We want to perform vacuum minimization first, before solvation and ionization.
 # NOTE: Gromacs no longer supports non-periodic boundary conditions (!!!),
 # so we must emulate a vacuum by using a very large (1000 Angstrom) box.
   - editconf:
       in:
-        input_crd_path: '*complex_vac.pdb'
+        input_crd_path: ~crd_path
         output_crd_path: '&complex_box.g96'
         config:
           box_type: cubic

examples/gromacs/tutorial.yml

@@ -4,6 +4,8 @@ steps:
   - modeling.yml:
   - stability.yml:
       in:
+        crd_path: '*complex_vac.pdb'
+        top_zip_path: '*complex_vac.zip'
         nsteps: 10000
         dt: 0.002
         temperature: 298.0

examples/scripts/Dockerfile_combine_structure

@@ -1,6 +1,6 @@
 FROM condaforge/mambaforge
 # NOT mambaforge-pypy3 (rdkit is incompatible with pypy)
 
-RUN mamba install -c conda-forge rdkit
+RUN mamba install -c conda-forge rdkit mdanalysis gromacs
 
 ADD combine_structure.py .