diff --git a/cwl_adapters/combine_structure.cwl b/cwl_adapters/combine_structure.cwl
index 4a8f6d50..f42c2266 100644
--- a/cwl_adapters/combine_structure.cwl
+++ b/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
diff --git a/examples/docking/docking.yml b/examples/docking/docking.yml
index a59bbd0f..380fe96d 100644
--- a/examples/docking/docking.yml
+++ b/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:
diff --git a/examples/docking/dsb.yml b/examples/docking/dsb.yml
index aec37dad..01794b07 100644
--- a/examples/docking/dsb.yml
+++ b/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):
diff --git a/examples/docking/gen_topol_params.yml b/examples/docking/gen_topol_params.yml
index 766b1270..863a1d38 100644
--- a/examples/docking/gen_topol_params.yml
+++ b/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:
diff --git a/examples/docking/vs_demo_2.yml b/examples/docking/vs_demo_2.yml
index 6c97a9b9..3c4274ae 100644
--- a/examples/docking/vs_demo_2.yml
+++ b/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):
diff --git a/examples/docking/vs_demo_3.yml b/examples/docking/vs_demo_3.yml
index 4202cc10..748d3aee 100644
--- a/examples/docking/vs_demo_3.yml
+++ b/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):
diff --git a/examples/docking/vs_demo_4.yml b/examples/docking/vs_demo_4.yml
index 7d0312e7..812312ad 100644
--- a/examples/docking/vs_demo_4.yml
+++ b/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):
diff --git a/examples/gromacs/basic.yml b/examples/gromacs/basic.yml
index 3cec70df..46294795 100644
--- a/examples/gromacs/basic.yml
+++ b/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:
diff --git a/examples/gromacs/cg.yml b/examples/gromacs/cg.yml
index 690222bc..42594d26 100644
--- a/examples/gromacs/cg.yml
+++ b/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
diff --git a/examples/gromacs/min.yml b/examples/gromacs/min.yml
index c1a36076..ad111e58 100644
--- a/examples/gromacs/min.yml
+++ b/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
diff --git a/examples/gromacs/setup.yml b/examples/gromacs/setup.yml
index 3738feb0..ff5c59a8 100644
--- a/examples/gromacs/setup.yml
+++ b/examples/gromacs/setup.yml
@@ -10,13 +10,6 @@ inputs:
     - edam:format_3987
 
 steps:
-# - editconf:
-#     in:
-#       input_crd_path: ~crd_path
-#       #input_crd_path: '*complex_vac.pdb'
-#       config:
-#         box_type: cubic
-#         distance_to_molecule: 1.2
 - gmx_editconf:
     in:
       input_crd_path: ~crd_path
diff --git a/examples/gromacs/setup_vac_min.yml b/examples/gromacs/setup_vac_min.yml
index 1be9c40f..6226f91e 100644
--- a/examples/gromacs/setup_vac_min.yml
+++ b/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
\ No newline at end of file
+    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'
diff --git a/examples/gromacs/solv_ion.yml b/examples/gromacs/solv_ion.yml
index f987b25a..691aa400 100644
--- a/examples/gromacs/solv_ion.yml
+++ b/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'
diff --git a/examples/gromacs/stability.yml b/examples/gromacs/stability.yml
index 76bfbc95..c9544bc4 100644
--- a/examples/gromacs/stability.yml
+++ b/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
diff --git a/examples/gromacs/steep.yml b/examples/gromacs/steep.yml
index 00e24f1e..ae5b80c8 100644
--- a/examples/gromacs/steep.yml
+++ b/examples/gromacs/steep.yml
@@ -1,3 +1,9 @@
+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!
@@ -5,6 +11,7 @@
 steps:
   - grompp:
       in:
+        input_top_zip_path: ~top_zip_path
         config:
           mdp:
             integrator: steep
diff --git a/examples/gromacs/topology.yml b/examples/gromacs/topology.yml
index 4b4c3843..fe686c7a 100644
--- a/examples/gromacs/topology.yml
+++ b/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
diff --git a/examples/gromacs/tutorial.yml b/examples/gromacs/tutorial.yml
index 8901e6c9..2b4d68bd 100644
--- a/examples/gromacs/tutorial.yml
+++ b/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
diff --git a/examples/scripts/Dockerfile_combine_structure b/examples/scripts/Dockerfile_combine_structure
index 973b0ee7..2e0b5591 100644
--- a/examples/scripts/Dockerfile_combine_structure
+++ b/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 .
\ No newline at end of file
diff --git a/examples/scripts/combine_structure.py b/examples/scripts/combine_structure.py
index f8a0f681..7ac06e3e 100644
--- a/examples/scripts/combine_structure.py
+++ b/examples/scripts/combine_structure.py
@@ -1,10 +1,16 @@
 import sys
 import os
+import zipfile
 import argparse
 from typing import Optional
 import numpy as np
 
 from rdkit import Chem
+import MDAnalysis as mda
+
+
+GROMACS_INCLUDE_PATH = os.path.realpath('/opt/conda/share/gromacs/top')
+TEMP_PATH = os.path.realpath('./')
 
 
 def parse_arguments() -> argparse.Namespace:
@@ -16,6 +22,7 @@ def parse_arguments() -> argparse.Namespace:
     parser = argparse.ArgumentParser()
     parser.add_argument('--input_structure1', required=True)
     parser.add_argument('--input_structure2', required=True)
+    parser.add_argument('--input_top_zip_path', required=True)
     parser.add_argument('--output_structure_path', required=True)
     args = parser.parse_args()
     return args
@@ -39,13 +46,34 @@ def read_xyz_rdkit(input_structure_path: str) -> Optional[Chem.rdchem.Mol]:
     return xyz
 
 
-def combine_structure_rdkit(input_structure1_path: str, input_structure2_path: str, output_structure_path: str) -> None:
-    """ Combine two structures into a single PDB file using RDKit
+def fix_atom_names(input_top_zip_path: str, output_structure_path: str) -> None:
+    """ Modifies the atom names based on the topology file
+
+    Args:
+        input_top_zip_path (str): The path to the input zip file
+        output_structure_path (str): The path to the output combined structure
+    """
+
+    with zipfile.ZipFile(input_top_zip_path, "r") as zip_read:
+        zip_read.extractall(path=TEMP_PATH)
+
+    file_list = [str(os.path.join(TEMP_PATH, f)) for f in zip_read.namelist()]
+    top_file = next(name for name in file_list if name.endswith(".top"))
+
+    u1 = mda.Universe(top_file, topology_format='ITP', include_dir=GROMACS_INCLUDE_PATH)
+    u2 = mda.Universe(os.path.join(TEMP_PATH, 'temp_out.pdb'))
+
+    u2.atoms.names = u1.atoms.names
+    all_atoms = u2.select_atoms("all")
+    all_atoms.write(output_structure_path)
+
+
+def combine_structure_rdkit(input_structure1_path: str, input_structure2_path: str) -> None:
+    """ Combine two structures into a single PDB file using RDKit and saves it in the temporary PDB file
 
     Args:
         input_structure1_path (str): The path to the xyz structure 1 
         input_structure2_path (str): The path to the xyz structure 2 
-        output_structure_path (str): The path to the output combined structure
     """
 
     structure1 = read_xyz_rdkit(input_structure1_path)
@@ -54,7 +82,7 @@ def combine_structure_rdkit(input_structure1_path: str, input_structure2_path: s
     if structure1 and structure2:
         combo = Chem.CombineMols(structure1, structure2)
 
-        with Chem.PDBWriter(output_structure_path) as writer:
+        with Chem.PDBWriter(os.path.join(TEMP_PATH, 'temp_out.pdb')) as writer:
             writer.write(combo)
 
 
@@ -71,7 +99,8 @@ def main() -> None:
         print(f'Error: Can not find file {args.input_structure2}')
         sys.exit(1)
 
-    combine_structure_rdkit(args.input_structure1, args.input_structure2, args.output_structure_path)
+    combine_structure_rdkit(args.input_structure1, args.input_structure2)
+    fix_atom_names(args.input_top_zip_path, args.output_structure_path)
 
 
 if __name__ == '__main__':