diff --git a/README.md b/README.md
index d7d58a0..18b74e5 100644
--- a/README.md
+++ b/README.md
@@ -3,7 +3,7 @@
 [![](https://img.shields.io/conda/vn/bioconda/biobb_gromacs?label=Conda)](https://anaconda.org/bioconda/biobb_gromacs)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_gromacs?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_gromacs)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_gromacs?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_gromacs:4.2.0--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_gromacs:5.0.0--pyhdfd78af_0)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_gromacs)
 [![](https://img.shields.io/pypi/pyversions/biobb-gromacs.svg?label=Python%20Versions)](https://pypi.org/project/biobb-gromacs/)
@@ -42,7 +42,7 @@ The latest documentation of this package can be found in our readthedocs site:
 [latest API documentation](http://biobb-gromacs.readthedocs.io/en/latest/).
 
 ### Version
-v4.2.0 2024.2
+v5.0.0 2024.2
 
 ### Installation
 Using PIP:
@@ -52,7 +52,7 @@ Using PIP:
 * Installation:
 
 
-        pip install "biobb_gromacs>=4.2.0"
+        pip install "biobb_gromacs>=5.0.0"
 
 
 * Usage: [Python API documentation](https://biobb-gromacs.readthedocs.io/en/latest/modules.html)
@@ -62,7 +62,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_gromacs>=4.2.0"
+        conda install -c bioconda "biobb_gromacs>=5.0.0"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-gromacs.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-gromacs.readthedocs.io/en/latest/command_line.html)
@@ -72,13 +72,13 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_gromacs:4.2.0--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_gromacs:5.0.0--pyhdfd78af_0
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_gromacs:4.2.0--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_gromacs:5.0.0--pyhdfd78af_0 <command>
 
 
 Using SINGULARITY:
@@ -88,7 +88,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_gromacs.sif https://depot.galaxyproject.org/singularity/biobb_gromacs:4.2.0--pyhdfd78af_0
+        singularity pull --name biobb_gromacs.sif https://depot.galaxyproject.org/singularity/biobb_gromacs:5.0.0--pyhdfd78af_0
 
 
 * Usage:
diff --git a/biobb_gromacs/__init__.py b/biobb_gromacs/__init__.py
index 77a8a50..235ee1c 100644
--- a/biobb_gromacs/__init__.py
+++ b/biobb_gromacs/__init__.py
@@ -1,6 +1,5 @@
-from . import gromacs
-from . import gromacs_extra
+from . import gromacs, gromacs_extra
 
 name = "biobb_gromacs"
 __all__ = ["gromacs", "gromacs_extra"]
-__version__ = "4.2.0"
+__version__ = "5.0.0"
diff --git a/biobb_gromacs/docs/source/change_log.md b/biobb_gromacs/docs/source/change_log.md
index 702a692..6f9c3bf 100644
--- a/biobb_gromacs/docs/source/change_log.md
+++ b/biobb_gromacs/docs/source/change_log.md
@@ -1,5 +1,22 @@
 # Biobb GROMACS changelog
 
+## What's new in version [5.0.0](https://github.com/bioexcel/biobb_gromacs/releases/tag/v5.0.0)?
+
+### Changes
+
+* [CI/CD](env.yaml): Update biobb_common version.
+* [Typing](ALL): Update typing from python 3.8 style to python 3.9
+* [CI/CD](conf.yml): Adding global properties to test yaml configuration
+* [CI/CD](linting_and_testing.yaml): Update GA test workflow to Python >3.9
+* [DOCS](.readthedocs.yaml): Updating to Python 3.9
+* [CI/CD](GITIGNORE): Update .gitignore to include the new file extensions to ignore
+* [CI/CD](conf.yml): Change test conf.yml to adapt to new settings configuration
+* [CI/CD](py.typed): Adding the py.typed
+* [FIX] Adding execution permissions to append_ligand
+* [UPDATE] Adding sandbox_path property to the json schemas
+* [FEATURE] New sandbox_path property
+* [CI/CD] Update grompp reference files and GA WF
+
 ## What's new in version [4.2.0](https://github.com/bioexcel/biobb_gromacs/releases/tag/v4.2.0)?
 
 ### Changes
diff --git a/biobb_gromacs/docs/source/conf.py b/biobb_gromacs/docs/source/conf.py
index 1832a1e..29368de 100644
--- a/biobb_gromacs/docs/source/conf.py
+++ b/biobb_gromacs/docs/source/conf.py
@@ -18,7 +18,7 @@
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-sys.path.insert(0, str(Path('../../').resolve()))
+sys.path.insert(0, str(Path("../../").resolve()))
 
 # -- General configuration ------------------------------------------------
 
@@ -29,14 +29,14 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.coverage',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.ifconfig',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.napoleon',
-    'sphinx_rtd_theme',
-    'recommonmark'
+    "sphinx.ext.autodoc",
+    "sphinx.ext.coverage",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.ifconfig",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.napoleon",
+    "sphinx_rtd_theme",
+    "recommonmark",
 ]
 
 # Using Google docstring style
@@ -44,7 +44,7 @@
 napoleon_google_docstring = True
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
@@ -55,7 +55,7 @@
 #    '.md': 'recommonmark.parser.CommonMarkParser',
 # }
 
-source_suffix = ['.rst', '.md']
+source_suffix = [".rst", ".md"]
 
 # source_suffix = {
 #    '.rst': 'restructuredtext',
@@ -66,21 +66,21 @@
 # source_encoding = 'utf-8-sig'
 
 # The master toctree document.
-master_doc = 'index'
+master_doc = "index"
 
 # General information about the project.
-project = u'biobb_gromacs'
-copyright = u'2024, Bioexcel Project'
-author = u'Bioexcel Project'
+project = "biobb_gromacs"
+copyright = "2024, Bioexcel Project"
+author = "Bioexcel Project"
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = u'4.2.0'
+version = "5.0.0"
 # The full version, including alpha/beta/rc tags.
-release = u'4.2.0'
+release = "5.0.0"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -97,7 +97,7 @@
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = []
+exclude_patterns: list = []
 
 # The reST default role (used for this markup: `text`) to use for all
 # documents.
@@ -115,7 +115,7 @@
 # show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 # A list of ignored prefixes for module index sorting.
 # modindex_common_prefix = []
@@ -129,14 +129,13 @@
 
 # -- Options for HTML output ----------------------------------------------
 def setup(app):
-
-    app.add_css_file('theme_overrides.css')
-    app.add_js_file('theme_overrides.js')
+    app.add_css_file("theme_overrides.css")
+    app.add_js_file("theme_overrides.js")
 
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -165,7 +164,7 @@ def setup(app):
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied
@@ -228,20 +227,17 @@ def setup(app):
 # html_search_scorer = 'scorer.js'
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'biobb_gromacs_doc'
+htmlhelp_basename = "biobb_gromacs_doc"
 
 # -- Options for LaTeX output ---------------------------------------------
 
-latex_elements = {
+latex_elements: dict = {
     # The paper size ('letterpaper' or 'a4paper').
     # 'papersize': 'letterpaper',
-
     # The font size ('10pt', '11pt' or '12pt').
     # 'pointsize': '10pt',
-
     # Additional stuff for the LaTeX preamble.
     # 'preamble': '',
-
     # Latex figure (float) alignment
     # 'figure_align': 'htbp',
 }
@@ -250,8 +246,13 @@ def setup(app):
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'biobb_gromacs.tex', u'biobb_gromacs Documentation',
-     u'Bioexcel Project', 'manual'),
+    (
+        master_doc,
+        "biobb_gromacs.tex",
+        "biobb_gromacs Documentation",
+        "Bioexcel Project",
+        "manual",
+    ),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -279,10 +280,7 @@ def setup(app):
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [
-    (master_doc, 'biobb_gromacs', u'biobb_gromacs Documentation',
-     [author], 1)
-]
+man_pages = [(master_doc, "biobb_gromacs", "biobb_gromacs Documentation", [author], 1)]
 
 # If true, show URL addresses after external links.
 # man_show_urls = False
@@ -294,10 +292,15 @@ def setup(app):
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'biobb_gromacs', u'biobb_gromacs Documentation',
-     author, 'biobb_gromacs',
-     'biobb_gromacs molecular dynamics building blocks',
-     'Miscellaneous'),
+    (
+        master_doc,
+        "biobb_gromacs",
+        "biobb_gromacs Documentation",
+        author,
+        "biobb_gromacs",
+        "biobb_gromacs molecular dynamics building blocks",
+        "Miscellaneous",
+    ),
 ]
 
 # Documents to append as an appendix to all manuals.
diff --git a/biobb_gromacs/docs/source/readme.md b/biobb_gromacs/docs/source/readme.md
index a34cf3a..18b74e5 100644
--- a/biobb_gromacs/docs/source/readme.md
+++ b/biobb_gromacs/docs/source/readme.md
@@ -3,7 +3,7 @@
 [![](https://img.shields.io/conda/vn/bioconda/biobb_gromacs?label=Conda)](https://anaconda.org/bioconda/biobb_gromacs)
 [![](https://img.shields.io/conda/dn/bioconda/biobb_gromacs?label=Conda%20Downloads)](https://anaconda.org/bioconda/biobb_gromacs)
 [![](https://img.shields.io/badge/Docker-Quay.io-blue)](https://quay.io/repository/biocontainers/biobb_gromacs?tab=tags)
-[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_gromacs:4.2.0--pyhdfd78af_0)
+[![](https://img.shields.io/badge/Singularity-GalaxyProject-blue)](https://depot.galaxyproject.org/singularity/biobb_gromacs:5.0.0--pyhdfd78af_0)
 
 [![](https://img.shields.io/badge/OS-Unix%20%7C%20MacOS-blue)](https://github.com/bioexcel/biobb_gromacs)
 [![](https://img.shields.io/pypi/pyversions/biobb-gromacs.svg?label=Python%20Versions)](https://pypi.org/project/biobb-gromacs/)
@@ -12,7 +12,7 @@
 
 [![](https://readthedocs.org/projects/biobb-gromacs/badge/?version=latest&label=Docs)](https://biobb-gromacs.readthedocs.io/en/latest/?badge=latest)
 [![](https://img.shields.io/website?down_message=Offline&label=Biobb%20Website&up_message=Online&url=https%3A%2F%2Fmmb.irbbarcelona.org%2Fbiobb%2F)](https://mmb.irbbarcelona.org/biobb/)
-[![](https://img.shields.io/badge/Youtube-tutorial-blue?logo=youtube&logoColor=red)](https://www.youtube.com/watch?v=ou1DOGNs0xM)
+[![](https://img.shields.io/badge/Youtube-tutorials-blue?logo=youtube&logoColor=red)](https://www.youtube.com/@BioExcelCoE/search?query=biobb)
 [![](https://zenodo.org/badge/DOI/10.1038/s41597-019-0177-4.svg)](https://doi.org/10.1038/s41597-019-0177-4)
 [![](https://img.shields.io/endpoint?color=brightgreen&url=https%3A%2F%2Fapi.juleskreuer.eu%2Fcitation-badge.php%3Fshield%26doi%3D10.1038%2Fs41597-019-0177-4)](https://www.nature.com/articles/s41597-019-0177-4#citeas)
 
@@ -42,7 +42,7 @@ The latest documentation of this package can be found in our readthedocs site:
 [latest API documentation](http://biobb-gromacs.readthedocs.io/en/latest/).
 
 ### Version
-v4.2.0 2024.2
+v5.0.0 2024.2
 
 ### Installation
 Using PIP:
@@ -52,7 +52,7 @@ Using PIP:
 * Installation:
 
 
-        pip install "biobb_gromacs>=4.2.0"
+        pip install "biobb_gromacs>=5.0.0"
 
 
 * Usage: [Python API documentation](https://biobb-gromacs.readthedocs.io/en/latest/modules.html)
@@ -62,7 +62,7 @@ Using ANACONDA:
 * Installation:
 
 
-        conda install -c bioconda "biobb_gromacs>=4.2.0"
+        conda install -c bioconda "biobb_gromacs>=5.0.0"
 
 
 * Usage: With conda installation BioBBs can be used with the [Python API documentation](https://biobb-gromacs.readthedocs.io/en/latest/modules.html) and the [Command Line documentation](https://biobb-gromacs.readthedocs.io/en/latest/command_line.html)
@@ -72,13 +72,13 @@ Using DOCKER:
 * Installation:
 
 
-        docker pull quay.io/biocontainers/biobb_gromacs:4.2.0--pyhdfd78af_0
+        docker pull quay.io/biocontainers/biobb_gromacs:5.0.0--pyhdfd78af_0
 
 
 * Usage:
 
 
-        docker run quay.io/biocontainers/biobb_gromacs:4.2.0--pyhdfd78af_0 <command>
+        docker run quay.io/biocontainers/biobb_gromacs:5.0.0--pyhdfd78af_0 <command>
 
 
 Using SINGULARITY:
@@ -88,7 +88,7 @@ Using SINGULARITY:
 * Installation:
 
 
-        singularity pull --name biobb_gromacs.sif https://depot.galaxyproject.org/singularity/biobb_gromacs:4.2.0--pyhdfd78af_0
+        singularity pull --name biobb_gromacs.sif https://depot.galaxyproject.org/singularity/biobb_gromacs:5.0.0--pyhdfd78af_0
 
 
 * Usage:
diff --git a/biobb_gromacs/docs/source/schema.html b/biobb_gromacs/docs/source/schema.html
index 29669e0..1bca1cc 100644
--- a/biobb_gromacs/docs/source/schema.html
+++ b/biobb_gromacs/docs/source/schema.html
@@ -10,7 +10,7 @@
   "applicationSubCategory": "http://www.edamontology.org/topic_3892",
   "citation": "https://www.nature.com/articles/s41597-019-0177-4",
   "license": "https://www.apache.org/licenses/LICENSE-2.0",
-  "softwareVersion": "4.2.0",
+  "softwareVersion": "5.0.0",
   "applicationSuite": "BioBB BioExcel Building Blocks",
   "codeRepository": "https://github.com/bioexcel/biobb_gromacs",
   "isAccessibleForFree": "True",
diff --git a/biobb_gromacs/gromacs/editconf.py b/biobb_gromacs/gromacs/editconf.py
index a6408fc..92debe4 100755
--- a/biobb_gromacs/gromacs/editconf.py
+++ b/biobb_gromacs/gromacs/editconf.py
@@ -1,14 +1,16 @@
 #!/usr/bin/env python3
 
 """Module containing the Editconf class and the command line interface."""
+
 import argparse
 from typing import Optional
-from biobb_common.generic.biobb_object import BiobbObject
+
 from biobb_common.configuration import settings
+from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.tools import file_utils as fu
 from biobb_common.tools.file_utils import launchlogger
+
 from biobb_gromacs.gromacs.common import get_gromacs_version
-from typing import Optional
 
 
 class Editconf(BiobbObject):
@@ -57,7 +59,13 @@ class Editconf(BiobbObject):
             * schema: http://edamontology.org/EDAM.owl
     """
 
-    def __init__(self, input_gro_path: str, output_gro_path: str, properties: Optional[dict] = None, **kwargs) -> None:
+    def __init__(
+        self,
+        input_gro_path: str,
+        output_gro_path: str,
+        properties: Optional[dict] = None,
+        **kwargs,
+    ) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -67,24 +75,24 @@ def __init__(self, input_gro_path: str, output_gro_path: str, properties: Option
         # Input/Output files
         self.io_dict = {
             "in": {"input_gro_path": input_gro_path},
-            "out": {"output_gro_path": output_gro_path}
+            "out": {"output_gro_path": output_gro_path},
         }
 
         # Properties specific for BB
-        self.distance_to_molecule = properties.get('distance_to_molecule', 1.0)
-        self.box_vector_lenghts = properties.get('box_vector_lenghts')
-        self.box_type = properties.get('box_type', 'cubic')
-        self.center_molecule = properties.get('center_molecule', True)
+        self.distance_to_molecule = properties.get("distance_to_molecule", 1.0)
+        self.box_vector_lenghts = properties.get("box_vector_lenghts")
+        self.box_type = properties.get("box_type", "cubic")
+        self.center_molecule = properties.get("center_molecule", True)
 
         # Properties common in all GROMACS BB
-        self.gmx_lib = properties.get('gmx_lib', None)
-        self.binary_path: str = properties.get('binary_path', 'gmx')
-        self.gmx_nobackup = properties.get('gmx_nobackup', True)
-        self.gmx_nocopyright = properties.get('gmx_nocopyright', True)
+        self.gmx_lib = properties.get("gmx_lib", None)
+        self.binary_path: str = properties.get("binary_path", "gmx")
+        self.gmx_nobackup = properties.get("gmx_nobackup", True)
+        self.gmx_nocopyright = properties.get("gmx_nocopyright", True)
         if self.gmx_nobackup:
-            self.binary_path += ' -nobackup'
+            self.binary_path += " -nobackup"
         if self.gmx_nocopyright:
-            self.binary_path += ' -nocopyright'
+            self.binary_path += " -nocopyright"
         if not self.container_path:
             self.gmx_version = get_gromacs_version(self.binary_path)
 
@@ -102,10 +110,16 @@ def launch(self) -> int:
         self.stage_files()
 
         # Create command line
-        self.cmd = [self.binary_path, 'editconf',
-                    '-f', self.stage_io_dict["in"]["input_gro_path"],
-                    '-o', self.stage_io_dict["out"]["output_gro_path"],
-                    '-bt', self.box_type]
+        self.cmd = [
+            self.binary_path,
+            "editconf",
+            "-f",
+            self.stage_io_dict["in"]["input_gro_path"],
+            "-o",
+            self.stage_io_dict["out"]["output_gro_path"],
+            "-bt",
+            self.box_type,
+        ]
 
         if self.box_vector_lenghts:
             if not isinstance(self.box_vector_lenghts, str):
@@ -113,13 +127,17 @@ def launch(self) -> int:
             self.cmd.append("-box")
             self.cmd.append(self.box_vector_lenghts)
         else:
-            self.cmd.append('-d')
+            self.cmd.append("-d")
             self.cmd.append(str(self.distance_to_molecule))
-            fu.log("Distance of the box to molecule: %6.2f" % self.distance_to_molecule, self.out_log, self.global_log)
+            fu.log(
+                "Distance of the box to molecule: %6.2f" % self.distance_to_molecule,
+                self.out_log,
+                self.global_log,
+            )
 
         if self.center_molecule:
-            self.cmd.append('-c')
-            fu.log('Centering molecule in the box.', self.out_log, self.global_log)
+            self.cmd.append("-c")
+            fu.log("Centering molecule in the box.", self.out_log, self.global_log)
 
         fu.log("Box type: %s" % self.box_type, self.out_log, self.global_log)
 
@@ -140,32 +158,51 @@ def launch(self) -> int:
         return self.return_code
 
 
-def editconf(input_gro_path: str, output_gro_path: str, properties: Optional[dict] = None, **kwargs) -> int:
+def editconf(
+    input_gro_path: str,
+    output_gro_path: str,
+    properties: Optional[dict] = None,
+    **kwargs,
+) -> int:
     """Create :class:`Editconf <gromacs.editconf.Editconf>` class and
     execute the :meth:`launch() <gromacs.editconf.Editconf.launch>` method."""
 
-    return Editconf(input_gro_path=input_gro_path, output_gro_path=output_gro_path,
-                    properties=properties, **kwargs).launch()
+    return Editconf(
+        input_gro_path=input_gro_path,
+        output_gro_path=output_gro_path,
+        properties=properties,
+        **kwargs,
+    ).launch()
 
 
 def main():
-    parser = argparse.ArgumentParser(description="Wrapper of the GROMACS gmx editconf module.",
-                                     formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
-    parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string")
+    parser = argparse.ArgumentParser(
+        description="Wrapper of the GROMACS gmx editconf module.",
+        formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999),
+    )
+    parser.add_argument(
+        "-c",
+        "--config",
+        required=False,
+        help="This file can be a YAML file, JSON file or JSON string",
+    )
 
     # Specific args of each building block
-    required_args = parser.add_argument_group('required arguments')
-    required_args.add_argument('--input_gro_path', required=True)
-    required_args.add_argument('--output_gro_path', required=True)
+    required_args = parser.add_argument_group("required arguments")
+    required_args.add_argument("--input_gro_path", required=True)
+    required_args.add_argument("--output_gro_path", required=True)
 
     args = parser.parse_args()
     config = args.config if args.config else None
     properties = settings.ConfReader(config=config).get_prop_dic()
 
     # Specific call of each building block
-    editconf(input_gro_path=args.input_gro_path, output_gro_path=args.output_gro_path,
-             properties=properties)
+    editconf(
+        input_gro_path=args.input_gro_path,
+        output_gro_path=args.output_gro_path,
+        properties=properties,
+    )
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()
diff --git a/biobb_gromacs/gromacs/genion.py b/biobb_gromacs/gromacs/genion.py
index 2683bbb..30060f9 100755
--- a/biobb_gromacs/gromacs/genion.py
+++ b/biobb_gromacs/gromacs/genion.py
@@ -1,16 +1,18 @@
 #!/usr/bin/env python3
 
 """Module containing the Genion class and the command line interface."""
-import shutil
+
 import argparse
-from typing import Optional
+import shutil
 from pathlib import Path
-from biobb_common.generic.biobb_object import BiobbObject
+from typing import Optional, Union
+
 from biobb_common.configuration import settings
+from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.tools import file_utils as fu
 from biobb_common.tools.file_utils import launchlogger
+
 from biobb_gromacs.gromacs.common import get_gromacs_version
-from typing import Optional, Union
 
 
 class Genion(BiobbObject):
@@ -64,8 +66,16 @@ class Genion(BiobbObject):
             * schema: http://edamontology.org/EDAM.owl
     """
 
-    def __init__(self, input_tpr_path: Union[str, Path], output_gro_path: Union[str, Path], input_top_zip_path: Union[str, Path],
-                 output_top_zip_path: Union[str, Path], input_ndx_path: Optional[Union[str, Path]] = None, properties: Optional[dict] = None, **kwargs) -> None:
+    def __init__(
+        self,
+        input_tpr_path: Union[str, Path],
+        output_gro_path: Union[str, Path],
+        input_top_zip_path: Union[str, Path],
+        output_top_zip_path: Union[str, Path],
+        input_ndx_path: Optional[Union[str, Path]] = None,
+        properties: Optional[dict] = None,
+        **kwargs,
+    ) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -75,23 +85,28 @@ def __init__(self, input_tpr_path: Union[str, Path], output_gro_path: Union[str,
         # Input/Output files
         self.io_dict = {
             "in": {"input_tpr_path": input_tpr_path, "input_ndx_path": input_ndx_path},
-            "out": {"output_gro_path": output_gro_path, "output_top_zip_path": output_top_zip_path}
+            "out": {
+                "output_gro_path": output_gro_path,
+                "output_top_zip_path": output_top_zip_path,
+            },
         }
         # Should not be copied inside container
         self.input_top_zip_path = input_top_zip_path
 
         # Properties specific for BB
-        self.output_top_path = properties.get('output_top_path', 'gio.top')  # Not in documentation for clarity
-        self.replaced_group = properties.get('replaced_group', 'SOL')
-        self.neutral = properties.get('neutral', False)
-        self.concentration = properties.get('concentration', 0.05)
-        self.seed = properties.get('seed', 1993)
+        self.output_top_path = properties.get(
+            "output_top_path", "gio.top"
+        )  # Not in documentation for clarity
+        self.replaced_group = properties.get("replaced_group", "SOL")
+        self.neutral = properties.get("neutral", False)
+        self.concentration = properties.get("concentration", 0.05)
+        self.seed = properties.get("seed", 1993)
 
         # Properties common in all GROMACS BB
-        self.gmx_lib = properties.get('gmx_lib', None)
-        self.binary_path = properties.get('binary_path', 'gmx')
-        self.gmx_nobackup = properties.get('gmx_nobackup', True)
-        self.gmx_nocopyright = properties.get('gmx_nocopyright', True)
+        self.gmx_lib = properties.get("gmx_lib", None)
+        self.binary_path = properties.get("binary_path", "gmx")
+        self.gmx_nobackup = properties.get("gmx_nobackup", True)
+        self.gmx_nocopyright = properties.get("gmx_nocopyright", True)
         if self.gmx_nobackup:
             self.binary_path = f"{self.binary_path} -nobackup"
         if self.gmx_nocopyright:
@@ -111,7 +126,9 @@ def launch(self) -> int:
         if self.check_restart():
             return 0
 
-        self.io_dict['in']['stdin_file_path'] = fu.create_stdin_file(f'{self.replaced_group}')
+        self.io_dict["in"]["stdin_file_path"] = fu.create_stdin_file(
+            f"{self.replaced_group}"
+        )
         self.stage_files()
 
         # Unzip topology to topology_out
@@ -119,37 +136,58 @@ def launch(self) -> int:
         top_dir = str(Path(top_file).parent)
 
         if self.container_path:
-            shutil.copytree(top_dir, Path(str(self.stage_io_dict.get("unique_dir", ""))).joinpath(Path(top_dir).name))
-            top_file = str(Path(self.container_volume_path).joinpath(Path(top_dir).name, Path(top_file).name))
-
-        self.cmd = [str(self.binary_path), 'genion',
-                    '-s', self.stage_io_dict["in"]["input_tpr_path"],
-                    '-o', self.stage_io_dict["out"]["output_gro_path"],
-                    '-p', top_file]
-
-        if self.stage_io_dict["in"].get("input_ndx_path") and Path(
-                self.stage_io_dict["in"].get("input_ndx_path")).exists():
-            self.cmd.append('-n')
+            shutil.copytree(
+                top_dir,
+                Path(str(self.stage_io_dict.get("unique_dir", ""))).joinpath(
+                    Path(top_dir).name
+                ),
+            )
+            top_file = str(
+                Path(self.container_volume_path).joinpath(
+                    Path(top_dir).name, Path(top_file).name
+                )
+            )
+
+        self.cmd = [
+            str(self.binary_path),
+            "genion",
+            "-s",
+            self.stage_io_dict["in"]["input_tpr_path"],
+            "-o",
+            self.stage_io_dict["out"]["output_gro_path"],
+            "-p",
+            top_file,
+        ]
+
+        if (
+            self.stage_io_dict["in"].get("input_ndx_path")
+            and Path(self.stage_io_dict["in"].get("input_ndx_path")).exists()
+        ):
+            self.cmd.append("-n")
             self.cmd.append(self.stage_io_dict["in"].get("input_ndx_path"))
 
         if self.neutral:
-            self.cmd.append('-neutral')
+            self.cmd.append("-neutral")
 
         if self.concentration:
-            self.cmd.append('-conc')
+            self.cmd.append("-conc")
             self.cmd.append(str(self.concentration))
-            fu.log('To reach up %g mol/litre concentration' % self.concentration, self.out_log, self.global_log)
+            fu.log(
+                "To reach up %g mol/litre concentration" % self.concentration,
+                self.out_log,
+                self.global_log,
+            )
 
         if self.seed is not None:
-            self.cmd.append('-seed')
+            self.cmd.append("-seed")
             self.cmd.append(str(self.seed))
 
         # Add stdin input file
-        self.cmd.append('<')
+        self.cmd.append("<")
         self.cmd.append(self.stage_io_dict["in"]["stdin_file_path"])
 
         if self.gmx_lib:
-            self.env_vars_dict['GMXLIB'] = self.gmx_lib
+            self.env_vars_dict["GMXLIB"] = self.gmx_lib
 
         # Run Biobb block
         self.run_biobb()
@@ -158,53 +196,96 @@ def launch(self) -> int:
         self.copy_to_host()
 
         if self.container_path:
-            top_file = str(Path(str(self.stage_io_dict.get("unique_dir", ""))).joinpath(Path(top_dir).name, Path(top_file).name))
+            top_file = str(
+                Path(str(self.stage_io_dict.get("unique_dir", ""))).joinpath(
+                    Path(top_dir).name, Path(top_file).name
+                )
+            )
 
         # zip topology
-        fu.log('Compressing topology to: %s' % self.stage_io_dict["out"]["output_top_zip_path"],
-               self.out_log, self.global_log)
-        fu.zip_top(zip_file=self.io_dict["out"]["output_top_zip_path"], top_file=top_file, out_log=self.out_log)
+        fu.log(
+            "Compressing topology to: %s"
+            % self.stage_io_dict["out"]["output_top_zip_path"],
+            self.out_log,
+            self.global_log,
+        )
+        fu.zip_top(
+            zip_file=self.io_dict["out"]["output_top_zip_path"],
+            top_file=top_file,
+            out_log=self.out_log,
+        )
 
         # Remove temporal files
-        self.tmp_files.extend([str(self.stage_io_dict.get("unique_dir", "")), top_dir, str(self.io_dict['in'].get("stdin_file_path"))])
+        self.tmp_files.extend(
+            [
+                str(self.stage_io_dict.get("unique_dir", "")),
+                top_dir,
+                str(self.io_dict["in"].get("stdin_file_path")),
+            ]
+        )
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=True)
         return self.return_code
 
 
-def genion(input_tpr_path: Union[str, Path], output_gro_path: Union[str, Path], input_top_zip_path: Union[str, Path],
-           output_top_zip_path: Union[str, Path], input_ndx_path: Optional[Union[str, Path]] = None, properties: Optional[dict] = None, **kwargs) -> int:
+def genion(
+    input_tpr_path: Union[str, Path],
+    output_gro_path: Union[str, Path],
+    input_top_zip_path: Union[str, Path],
+    output_top_zip_path: Union[str, Path],
+    input_ndx_path: Optional[Union[str, Path]] = None,
+    properties: Optional[dict] = None,
+    **kwargs,
+) -> int:
     """Create :class:`Genion <gromacs.genion.Genion>` class and
-        execute the :meth:`launch() <gromacs.genion.Genion.launch>` method."""
-    return Genion(input_tpr_path=input_tpr_path, output_gro_path=output_gro_path,
-                  input_top_zip_path=input_top_zip_path, output_top_zip_path=output_top_zip_path,
-                  input_ndx_path=input_ndx_path, properties=properties, **kwargs).launch()
+    execute the :meth:`launch() <gromacs.genion.Genion.launch>` method."""
+    return Genion(
+        input_tpr_path=input_tpr_path,
+        output_gro_path=output_gro_path,
+        input_top_zip_path=input_top_zip_path,
+        output_top_zip_path=output_top_zip_path,
+        input_ndx_path=input_ndx_path,
+        properties=properties,
+        **kwargs,
+    ).launch()
 
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""
-    parser = argparse.ArgumentParser(description="Wrapper for the GROMACS genion module.",
-                                     formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
-    parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string")
+    parser = argparse.ArgumentParser(
+        description="Wrapper for the GROMACS genion module.",
+        formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999),
+    )
+    parser.add_argument(
+        "-c",
+        "--config",
+        required=False,
+        help="This file can be a YAML file, JSON file or JSON string",
+    )
 
     # Specific args of each building block
-    required_args = parser.add_argument_group('required arguments')
-    required_args.add_argument('--input_tpr_path', required=True)
-    required_args.add_argument('--output_gro_path', required=True)
-    required_args.add_argument('--input_top_zip_path', required=True)
-    required_args.add_argument('--output_top_zip_path', required=True)
-    parser.add_argument('--input_ndx_path', required=False)
+    required_args = parser.add_argument_group("required arguments")
+    required_args.add_argument("--input_tpr_path", required=True)
+    required_args.add_argument("--output_gro_path", required=True)
+    required_args.add_argument("--input_top_zip_path", required=True)
+    required_args.add_argument("--output_top_zip_path", required=True)
+    parser.add_argument("--input_ndx_path", required=False)
 
     args = parser.parse_args()
     config = args.config if args.config else None
     properties = settings.ConfReader(config=config).get_prop_dic()
 
     # Specific call of each building block
-    genion(input_tpr_path=args.input_tpr_path, output_gro_path=args.output_gro_path,
-           input_top_zip_path=args.input_top_zip_path, output_top_zip_path=args.output_top_zip_path,
-           input_ndx_path=args.input_ndx_path, properties=properties)
+    genion(
+        input_tpr_path=args.input_tpr_path,
+        output_gro_path=args.output_gro_path,
+        input_top_zip_path=args.input_top_zip_path,
+        output_top_zip_path=args.output_top_zip_path,
+        input_ndx_path=args.input_ndx_path,
+        properties=properties,
+    )
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()
diff --git a/biobb_gromacs/gromacs/genrestr.py b/biobb_gromacs/gromacs/genrestr.py
index 5215ecb..0ebf47b 100755
--- a/biobb_gromacs/gromacs/genrestr.py
+++ b/biobb_gromacs/gromacs/genrestr.py
@@ -1,15 +1,17 @@
 #!/usr/bin/env python3
 
 """Module containing the Genrestr class and the command line interface."""
+
 import argparse
-from typing import Optional
-from biobb_common.generic.biobb_object import BiobbObject
+from pathlib import Path
+from typing import Optional, Union
+
 from biobb_common.configuration import settings
+from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.tools import file_utils as fu
 from biobb_common.tools.file_utils import launchlogger
+
 from biobb_gromacs.gromacs.common import get_gromacs_version
-from pathlib import Path
-from typing import Union, Optional
 
 
 class Genrestr(BiobbObject):
@@ -57,8 +59,14 @@ class Genrestr(BiobbObject):
             * schema: http://edamontology.org/EDAM.owl
     """
 
-    def __init__(self, input_structure_path: Union[str, Path], output_itp_path: Union[str, Path],
-                 input_ndx_path: Optional[Union[str, Path]] = None, properties: Optional[dict] = None, **kwargs) -> None:
+    def __init__(
+        self,
+        input_structure_path: Union[str, Path],
+        output_itp_path: Union[str, Path],
+        input_ndx_path: Optional[Union[str, Path]] = None,
+        properties: Optional[dict] = None,
+        **kwargs,
+    ) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -67,19 +75,22 @@ def __init__(self, input_structure_path: Union[str, Path], output_itp_path: Unio
 
         # Input/Output files
         self.io_dict = {
-            "in": {"input_structure_path": input_structure_path, "input_ndx_path": input_ndx_path},
-            "out": {"output_itp_path": output_itp_path}
+            "in": {
+                "input_structure_path": input_structure_path,
+                "input_ndx_path": input_ndx_path,
+            },
+            "out": {"output_itp_path": output_itp_path},
         }
 
         # Properties specific for BB
-        self.force_constants = str(properties.get('force_constants', '500 500 500'))
-        self.restrained_group = properties.get('restrained_group', 'system')
+        self.force_constants = str(properties.get("force_constants", "500 500 500"))
+        self.restrained_group = properties.get("restrained_group", "system")
 
         # Properties common in all GROMACS BB
-        self.gmx_lib = properties.get('gmx_lib', None)
-        self.binary_path = properties.get('binary_path', 'gmx')
-        self.gmx_nobackup = properties.get('gmx_nobackup', True)
-        self.gmx_nocopyright = properties.get('gmx_nocopyright', True)
+        self.gmx_lib = properties.get("gmx_lib", None)
+        self.binary_path = properties.get("binary_path", "gmx")
+        self.gmx_nobackup = properties.get("gmx_nobackup", True)
+        self.gmx_nocopyright = properties.get("gmx_nocopyright", True)
         if self.gmx_nobackup:
             self.binary_path = f"{self.binary_path}  -nobackup"
         if self.gmx_nocopyright:
@@ -99,12 +110,19 @@ def launch(self) -> int:
         if self.check_restart():
             return 0
 
-        self.io_dict['in']['stdin_file_path'] = fu.create_stdin_file(f'{self.restrained_group}')
+        self.io_dict["in"]["stdin_file_path"] = fu.create_stdin_file(
+            f"{self.restrained_group}"
+        )
         self.stage_files()
 
-        self.cmd = [str(self.binary_path), "genrestr",
-                    "-f", self.stage_io_dict["in"]["input_structure_path"],
-                    "-o", self.stage_io_dict["out"]["output_itp_path"]]
+        self.cmd = [
+            str(self.binary_path),
+            "genrestr",
+            "-f",
+            self.stage_io_dict["in"]["input_structure_path"],
+            "-o",
+            self.stage_io_dict["out"]["output_itp_path"],
+        ]
 
         if not isinstance(self.force_constants, str):
             self.force_constants = " ".join(map(str, self.force_constants))
@@ -113,15 +131,15 @@ def launch(self) -> int:
         self.cmd.append(self.force_constants)
 
         if self.stage_io_dict["in"].get("input_ndx_path"):
-            self.cmd.append('-n')
+            self.cmd.append("-n")
             self.cmd.append(self.stage_io_dict["in"]["input_ndx_path"])
 
         # Add stdin input file
-        self.cmd.append('<')
+        self.cmd.append("<")
         self.cmd.append(self.stage_io_dict["in"]["stdin_file_path"])
 
         if self.gmx_lib:
-            self.env_vars_dict['GMXLIB'] = self.gmx_lib
+            self.env_vars_dict["GMXLIB"] = self.gmx_lib
 
         # Run Biobb block
         self.run_biobb()
@@ -130,42 +148,68 @@ def launch(self) -> int:
         self.copy_to_host()
 
         # Remove temporal files
-        self.tmp_files.extend([str(self.stage_io_dict.get("unique_dir", "")), str(self.io_dict['in'].get("stdin_file_path"))])
+        self.tmp_files.extend(
+            [
+                str(self.stage_io_dict.get("unique_dir", "")),
+                str(self.io_dict["in"].get("stdin_file_path")),
+            ]
+        )
         self.remove_tmp_files()
 
         self.check_arguments(output_files_created=True, raise_exception=False)
         return self.return_code
 
 
-def genrestr(input_structure_path: Union[str, Path], output_itp_path: Union[str, Path],
-             input_ndx_path: Optional[Union[str, Path]] = None, properties: Optional[dict] = None, **kwargs) -> int:
+def genrestr(
+    input_structure_path: Union[str, Path],
+    output_itp_path: Union[str, Path],
+    input_ndx_path: Optional[Union[str, Path]] = None,
+    properties: Optional[dict] = None,
+    **kwargs,
+) -> int:
     """Create :class:`Genrestr <gromacs.genrestr.Genrestr>` class and
     execute the :meth:`launch() <gromacs.genrestr.Genrestr.launch>` method."""
 
-    return Genrestr(input_structure_path=input_structure_path, output_itp_path=output_itp_path,
-                    input_ndx_path=input_ndx_path, properties=properties, **kwargs).launch()
+    return Genrestr(
+        input_structure_path=input_structure_path,
+        output_itp_path=output_itp_path,
+        input_ndx_path=input_ndx_path,
+        properties=properties,
+        **kwargs,
+    ).launch()
 
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""
-    parser = argparse.ArgumentParser(description="Wrapper for the GROMACS genion module.",
-                                     formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
-    parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string")
+    parser = argparse.ArgumentParser(
+        description="Wrapper for the GROMACS genion module.",
+        formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999),
+    )
+    parser.add_argument(
+        "-c",
+        "--config",
+        required=False,
+        help="This file can be a YAML file, JSON file or JSON string",
+    )
 
     # Specific args of each building block
-    required_args = parser.add_argument_group('required arguments')
-    required_args.add_argument('--input_structure_path', required=True)
-    required_args.add_argument('--output_itp_path', required=True)
-    parser.add_argument('--input_ndx_path', required=False)
+    required_args = parser.add_argument_group("required arguments")
+    required_args.add_argument("--input_structure_path", required=True)
+    required_args.add_argument("--output_itp_path", required=True)
+    parser.add_argument("--input_ndx_path", required=False)
 
     args = parser.parse_args()
     config = args.config if args.config else None
     properties = settings.ConfReader(config=config).get_prop_dic()
 
     # Specific call of each building block
-    genrestr(input_structure_path=args.input_structure_path, input_ndx_path=args.input_ndx_path,
-             output_itp_path=args.output_itp_path, properties=properties)
+    genrestr(
+        input_structure_path=args.input_structure_path,
+        input_ndx_path=args.input_ndx_path,
+        output_itp_path=args.output_itp_path,
+        properties=properties,
+    )
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()
diff --git a/biobb_gromacs/gromacs_extra/append_ligand.py b/biobb_gromacs/gromacs_extra/append_ligand.py
index ce78977..c45a143 100755
--- a/biobb_gromacs/gromacs_extra/append_ligand.py
+++ b/biobb_gromacs/gromacs_extra/append_ligand.py
@@ -1,14 +1,15 @@
 #!/usr/bin/env python3
 
 """Module containing the AppendLigand class and the command line interface."""
-import re
+
 import argparse
-from typing import Optional
+import re
 import shutil
 from pathlib import Path
 from typing import Optional
-from biobb_common.generic.biobb_object import BiobbObject
+
 from biobb_common.configuration import settings
+from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.tools import file_utils as fu
 from biobb_common.tools.file_utils import launchlogger
 
@@ -49,8 +50,15 @@ class AppendLigand(BiobbObject):
             * schema: http://edamontology.org/EDAM.owl
     """
 
-    def __init__(self, input_top_zip_path: str, input_itp_path: str, output_top_zip_path: str,
-                 input_posres_itp_path: Optional[str] = None, properties: Optional[dict] = None, **kwargs) -> None:
+    def __init__(
+        self,
+        input_top_zip_path: str,
+        input_itp_path: str,
+        output_top_zip_path: str,
+        input_posres_itp_path: Optional[str] = None,
+        properties: Optional[dict] = None,
+        **kwargs,
+    ) -> None:
         properties = properties or {}
 
         # Call parent class constructor
@@ -59,13 +67,16 @@ def __init__(self, input_top_zip_path: str, input_itp_path: str, output_top_zip_
 
         # Input/Output files
         self.io_dict = {
-            "in": {"input_top_zip_path": input_top_zip_path, "input_itp_path": input_itp_path,
-                   "input_posres_itp_path": input_posres_itp_path},
-            "out": {"output_top_zip_path": output_top_zip_path}
+            "in": {
+                "input_top_zip_path": input_top_zip_path,
+                "input_itp_path": input_itp_path,
+                "input_posres_itp_path": input_posres_itp_path,
+            },
+            "out": {"output_top_zip_path": output_top_zip_path},
         }
 
         # Properties specific for BB
-        self.posres_name = properties.get('posres_name', 'POSRES_LIGAND')
+        self.posres_name = properties.get("posres_name", "POSRES_LIGAND")
 
         # Check the properties
         self.check_properties(properties)
@@ -79,74 +90,103 @@ def launch(self) -> int:
             return 0
 
         # Unzip topology
-        top_file = fu.unzip_top(zip_file=str(self.io_dict['in'].get("input_top_zip_path")), out_log=self.out_log)
+        top_file = fu.unzip_top(
+            zip_file=str(self.io_dict["in"].get("input_top_zip_path")),
+            out_log=self.out_log,
+        )
         top_dir = str(Path(top_file).parent)
-        itp_name = str(Path(str(self.io_dict['in'].get("input_itp_path"))).name)
+        itp_name = str(Path(str(self.io_dict["in"].get("input_itp_path"))).name)
 
         with open(top_file) as top_f:
             top_lines = top_f.readlines()
             top_f.close()
         fu.rm(top_file)
 
-        forcefield_pattern = r'#include.*forcefield.itp\"'
+        forcefield_pattern = r"#include.*forcefield.itp\""
         if top_lines:
             for index, line in enumerate(top_lines):
                 if re.search(forcefield_pattern, line):
                     break
         else:
-            fu.log(f'FATAL: Input topfile {top_file} from input_top_zip_path {self.io_dict["in"].get("input_top_zip_path")} is empty.', self.out_log, self.global_log)
+            fu.log(
+                f'FATAL: Input topfile {top_file} from input_top_zip_path {self.io_dict["in"].get("input_top_zip_path")} is empty.',
+                self.out_log,
+                self.global_log,
+            )
             return 1
 
-        top_lines.insert(index+1, '\n')
-        top_lines.insert(index+2, '; Including ligand ITP\n')
-        top_lines.insert(index+3, '#include "' + itp_name + '"\n')
-        top_lines.insert(index+4, '\n')
-        if self.io_dict['in'].get("input_posres_itp_path"):
-            top_lines.insert(index+5, '; Ligand position restraints'+'\n')
-            top_lines.insert(index+6, '#ifdef '+self.posres_name+'\n')
-            top_lines.insert(index+7, '#include "'+str(Path(self.io_dict['in'].get("input_posres_itp_path", "")).name)+'"\n')
-            top_lines.insert(index+8, '#endif'+'\n')
-            top_lines.insert(index+9, '\n')
+        top_lines.insert(index + 1, "\n")
+        top_lines.insert(index + 2, "; Including ligand ITP\n")
+        top_lines.insert(index + 3, '#include "' + itp_name + '"\n')
+        top_lines.insert(index + 4, "\n")
+        if self.io_dict["in"].get("input_posres_itp_path"):
+            top_lines.insert(index + 5, "; Ligand position restraints" + "\n")
+            top_lines.insert(index + 6, "#ifdef " + self.posres_name + "\n")
+            top_lines.insert(
+                index + 7,
+                '#include "'
+                + str(Path(self.io_dict["in"].get("input_posres_itp_path", "")).name)
+                + '"\n',
+            )
+            top_lines.insert(index + 8, "#endif" + "\n")
+            top_lines.insert(index + 9, "\n")
 
         inside_moleculetype_section = False
-        with open(self.io_dict['in'].get("input_itp_path", "")) as itp_file:
-            moleculetype_pattern = r'\[ moleculetype \]'
+        with open(self.io_dict["in"].get("input_itp_path", "")) as itp_file:
+            moleculetype_pattern = r"\[ moleculetype \]"
             for line in itp_file:
                 if re.search(moleculetype_pattern, line):
                     inside_moleculetype_section = True
                     continue
-                if inside_moleculetype_section and not line.startswith(';'):
+                if inside_moleculetype_section and not line.startswith(";"):
                     moleculetype = line.strip().split()[0].strip()
                     break
 
-        molecules_pattern = r'\[ molecules \]'
+        molecules_pattern = r"\[ molecules \]"
         inside_molecules_section = False
         index_molecule = None
-        molecule_string = str(moleculetype)+int(20-len(moleculetype))*' '+'1'+'\n'
+        molecule_string = (
+            str(moleculetype) + int(20 - len(moleculetype)) * " " + "1" + "\n"
+        )
         for index, line in enumerate(top_lines):
             if re.search(molecules_pattern, line):
                 inside_molecules_section = True
                 continue
-            if inside_molecules_section and not line.startswith(';') and line.upper().startswith('PROTEIN'):
+            if (
+                inside_molecules_section
+                and not line.startswith(";")
+                and line.upper().startswith("PROTEIN")
+            ):
                 index_molecule = index
 
         if index_molecule:
-            top_lines.insert(index_molecule+1, molecule_string)
+            top_lines.insert(index_molecule + 1, molecule_string)
         else:
             top_lines.append(molecule_string)
 
-        new_top = fu.create_name(path=top_dir, prefix=self.prefix, step=self.step, name='ligand.top')
+        new_top = fu.create_name(
+            path=top_dir, prefix=self.prefix, step=self.step, name="ligand.top"
+        )
 
-        with open(new_top, 'w') as new_top_f:
+        with open(new_top, "w") as new_top_f:
             new_top_f.write("".join(top_lines))
 
-        shutil.copy2(self.io_dict['in'].get("input_itp_path", ""), top_dir)
-        if self.io_dict['in'].get("input_posres_itp_path"):
-            shutil.copy2(self.io_dict['in'].get("input_posres_itp_path", ""), top_dir)
+        shutil.copy2(self.io_dict["in"].get("input_itp_path", ""), top_dir)
+        if self.io_dict["in"].get("input_posres_itp_path"):
+            shutil.copy2(self.io_dict["in"].get("input_posres_itp_path", ""), top_dir)
 
         # zip topology
-        fu.log('Compressing topology to: %s' % self.io_dict['out'].get("output_top_zip_path"), self.out_log, self.global_log)
-        fu.zip_top(zip_file=self.io_dict['out'].get("output_top_zip_path", ""), top_file=new_top, out_log=self.out_log)
+        fu.log(
+            "Compressing topology to: %s"
+            % self.io_dict["out"].get("output_top_zip_path"),
+            self.out_log,
+            self.global_log,
+        )
+        fu.zip_top(
+            zip_file=self.io_dict["out"].get("output_top_zip_path", ""),
+            top_file=new_top,
+            out_log=self.out_log,
+        )
 
         # Remove temporal files
         self.tmp_files.append(top_dir)
@@ -156,39 +196,59 @@ def launch(self) -> int:
         return 0
 
 
-def append_ligand(input_top_zip_path: str, input_itp_path: str, output_top_zip_path: str,
-                  input_posres_itp_path: Optional[str] = None, properties: Optional[dict] = None, **kwargs) -> int:
+def append_ligand(
+    input_top_zip_path: str,
+    input_itp_path: str,
+    output_top_zip_path: str,
+    input_posres_itp_path: Optional[str] = None,
+    properties: Optional[dict] = None,
+    **kwargs,
+) -> int:
     """Create :class:`AppendLigand <gromacs_extra.append_ligand.AppendLigand>` class and
     execute the :meth:`launch() <gromacs_extra.append_ligand.AppendLigand.launch>` method."""
-    return AppendLigand(input_top_zip_path=input_top_zip_path,
-                        input_itp_path=input_itp_path,
-                        output_top_zip_path=output_top_zip_path,
-                        input_posres_itp_path=input_posres_itp_path,
-                        properties=properties, **kwargs).launch()
+    return AppendLigand(
+        input_top_zip_path=input_top_zip_path,
+        input_itp_path=input_itp_path,
+        output_top_zip_path=output_top_zip_path,
+        input_posres_itp_path=input_posres_itp_path,
+        properties=properties,
+        **kwargs,
+    ).launch()
 
 
 def main():
     """Command line execution of this building block. Please check the command line documentation."""
-    parser = argparse.ArgumentParser(description="Wrapper of the GROMACS editconf module.",
-                                     formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
-    parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string")
+    parser = argparse.ArgumentParser(
+        description="Wrapper of the GROMACS editconf module.",
+        formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999),
+    )
+    parser.add_argument(
+        "-c",
+        "--config",
+        required=False,
+        help="This file can be a YAML file, JSON file or JSON string",
+    )
 
     # Specific args of each building block
-    required_args = parser.add_argument_group('required arguments')
-    required_args.add_argument('--input_top_zip_path', required=True)
-    required_args.add_argument('--input_itp_path', required=True)
-    required_args.add_argument('--output_top_zip_path', required=True)
-    parser.add_argument('--input_posres_itp_path', required=False)
+    required_args = parser.add_argument_group("required arguments")
+    required_args.add_argument("--input_top_zip_path", required=True)
+    required_args.add_argument("--input_itp_path", required=True)
+    required_args.add_argument("--output_top_zip_path", required=True)
+    parser.add_argument("--input_posres_itp_path", required=False)
 
     args = parser.parse_args()
     config = args.config if args.config else None
     properties = settings.ConfReader(config=config).get_prop_dic()
 
     # Specific call of each building block
-    append_ligand(input_top_zip_path=args.input_top_zip_path, input_itp_path=args.input_itp_path,
-                  output_top_zip_path=args.output_top_zip_path, input_posres_itp_path=args.input_posres_itp_path,
-                  properties=properties)
+    append_ligand(
+        input_top_zip_path=args.input_top_zip_path,
+        input_itp_path=args.input_itp_path,
+        output_top_zip_path=args.output_top_zip_path,
+        input_posres_itp_path=args.input_posres_itp_path,
+        properties=properties,
+    )
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     main()
diff --git a/biobb_gromacs/json_schemas/biobb_gromacs.json b/biobb_gromacs/json_schemas/biobb_gromacs.json
index 3e059cd..517d621 100644
--- a/biobb_gromacs/json_schemas/biobb_gromacs.json
+++ b/biobb_gromacs/json_schemas/biobb_gromacs.json
@@ -4,9 +4,9 @@
     "github": "https://github.com/bioexcel/biobb_gromacs",
     "readthedocs": "https://biobb-gromacs.readthedocs.io/en/latest/",
     "conda": "https://anaconda.org/bioconda/biobb_gromacs",
-    "docker": "https://quay.io/biocontainers/biobb_gromacs:4.2.0--pyhdfd78af_0",
-    "singularity": "https://depot.galaxyproject.org/singularity/biobb_gromacs:4.2.0--pyhdfd78af_0",
-    "version": "4.2.0",
+    "docker": "https://quay.io/biocontainers/biobb_gromacs:5.0.0--pyhdfd78af_0",
+    "singularity": "https://depot.galaxyproject.org/singularity/biobb_gromacs:5.0.0--pyhdfd78af_0",
+    "version": "5.0.0",
     "rest": false,
     "tools": [
         {
@@ -115,12 +115,12 @@
         }
     ],
     "dep_pypi": [
-        "install_requires=['biobb_common==4.2.0']",
-        "python_requires='>=3.8'"
+        "install_requires=['biobb_common==5.0.0']",
+        "python_requires='>=3.9'"
     ],
     "dep_conda": [
-        "python >=3.8",
-        "biobb_common ==4.2.0",
+        "python >=3.9",
+        "biobb_common ==5.0.0",
         "gromacs=2022.2=nompi_h1c20066_100"
     ],
     "keywords": [
diff --git a/setup.py b/setup.py
index 0a51ecb..46c0802 100644
--- a/setup.py
+++ b/setup.py
@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="biobb_gromacs",
-    version="4.2.0",
+    version="5.0.0",
     author="Biobb developers",
     author_email="pau.andrio@bsc.es",
     description="biobb_gromacs is the Biobb module collection to perform molecular dynamics simulations.",
@@ -15,12 +15,12 @@
     url="https://github.com/bioexcel/biobb_gromacs",
     project_urls={
         "Documentation": "http://biobb-gromacs.readthedocs.io/en/latest/",
-        "Bioexcel": "https://bioexcel.eu/"
+        "Bioexcel": "https://bioexcel.eu/",
     },
-    packages=setuptools.find_packages(exclude=['docs', 'test']),
-    package_data={'biobb_gromacs': ['py.typed']},
-    install_requires=['biobb_common==4.2.0'],
-    python_requires='>=3.8',
+    packages=setuptools.find_packages(exclude=["docs", "test"]),
+    package_data={"biobb_gromacs": ["py.typed"]},
+    install_requires=["biobb_common==5.0.0"],
+    python_requires=">=3.9",
     entry_points={
         "console_scripts": [
             "editconf = biobb_gromacs.gromacs.editconf:main",
@@ -35,17 +35,15 @@
             "solvate = biobb_gromacs.gromacs.solvate:main",
             "trjcat = biobb_gromacs.gromacs.trjcat:main",
             "ndx2resttop = biobb_gromacs.gromacs_extra.ndx2resttop:main",
-            "append_ligand = biobb_gromacs.gromacs_extra.append_ligand:main"
+            "append_ligand = biobb_gromacs.gromacs_extra.append_ligand:main",
         ]
     },
     classifiers=[
         "Development Status :: 5 - Production/Stable",
-        "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
-        "Programming Language :: Python :: 3.10",
         "License :: OSI Approved :: Apache Software License",
         "Operating System :: MacOS :: MacOS X",
         "Operating System :: POSIX",
-        "Operating System :: Unix"
+        "Operating System :: Unix",
     ],
 )