Documentation

README.md

@@ -1,3 +1,4 @@
+[![](https://readthedocs.org/projects/biobb-wf-ligand-parameterization/badge/?version=latest)](https://biobb-wf-ligand-parameterization.readthedocs.io/en/latest/?badge=latest)
 
 # Automatic Ligand parameterization tutorial using BioExcel Building Blocks (biobb)
 
@@ -13,6 +14,7 @@ This tutorial aims to illustrate the process of **ligand parameterization** for
 
 ### Biobb modules used
 
+* [biobb_io](https://github.com/bioexcel/biobb_io): Tools to fetch data to be consumed by the rest of the Biobb building blocks.
 * [biobb_chemistry](https://github.com/bioexcel/biobb_chemistry): Tools to manipulate chemical data.
 
 ### Auxiliar libraries used
@@ -30,7 +32,7 @@ conda install -c bioconda biobb_ligand_parameterization //// NOTE: this is not y
 
 ## Tutorial
 
-Click here to [view tutorial in Read the Docs]()
+Click here to [view tutorial in Read the Docs](https://biobb-wf-ligand-parameterization.readthedocs.io/en/latest/index.html)
 
 ***
 

biobb_wf_ligand_parameterization/docs/source/readme.md

@@ -1,3 +1,4 @@
+[![](https://readthedocs.org/projects/biobb-wf-ligand-parameterization/badge/?version=latest)](https://biobb-wf-ligand-parameterization.readthedocs.io/en/latest/?badge=latest)
 
 # Automatic Ligand parameterization tutorial using BioExcel Building Blocks (biobb)
 
@@ -13,6 +14,7 @@ This tutorial aims to illustrate the process of **ligand parameterization** for
 
 ### Biobb modules used
 
+* [biobb_io](https://github.com/bioexcel/biobb_io): Tools to fetch data to be consumed by the rest of the Biobb building blocks.
 * [biobb_chemistry](https://github.com/bioexcel/biobb_chemistry): Tools to manipulate chemical data.
 
 ### Auxiliar libraries used
@@ -30,7 +32,7 @@ conda install -c bioconda biobb_ligand_parameterization //// NOTE: this is not y
 
 ## Tutorial
 
-Click here to [view tutorial in Read the Docs]()
+Click here to [view tutorial in Read the Docs](https://biobb-wf-ligand-parameterization.readthedocs.io/en/latest/index.html)
 
 ***
 

biobb_wf_ligand_parameterization/docs/source/tutorial.md

@@ -30,7 +30,8 @@ Conda **Installation**:
  6. [Output Files](#output)
 
 ***
-![Bioexcel2_logo_400px_transp.png](attachment:Bioexcel2_logo_400px_transp.png)
+<img src="https://bioexcel.eu/wp-content/uploads/2019/04/Bioexcell_logo_1080px_transp.png" alt="Bioexcel2 logo"
+    title="Bioexcel2 logo" width="400" />
 ***
 
 <a id="input"></a>
@@ -272,5 +273,5 @@ view
 
 Important **Output files** generated:
  - IBPparams.gro: **Structure** of the parameterized ligand in gro (GROMACS) format.
- - IBPparams.top: **Topology** of the parameterized ligand, including a reference to the {{output_acpype_itp}}.
+ - IBPparams.top: **Topology** of the parameterized ligand, including a reference to the IBPparams.itp.
  - IBPparams.itp: **Include Topology File (itp)** of the parameterized ligand, including the parameters information: bonds, angles, dihedrals, etc.

biobb_wf_ligand_parameterization/html/biobb_ligand_parameterization_tutorial.web.html

@@ -13561,7 +13561,7 @@ <h3 id="Visualizing-3D-structure">Visualizing 3D structure<a class="anchor-link"
 <h2 id="Output-files">Output files<a class="anchor-link" href="#Output-files">&#182;</a></h2><p>Important <strong>Output files</strong> generated:</p>
 <ul>
 <li>IBPparams.gro: <strong>Structure</strong> of the parameterized ligand in gro (GROMACS) format.</li>
-<li>IBPparams.top: <strong>Topology</strong> of the parameterized ligand, including a reference to the {{output_acpype_itp}}.</li>
+<li>IBPparams.top: <strong>Topology</strong> of the parameterized ligand, including a reference to the IBPparams.itp.</li>
 <li>IBPparams.itp: <strong>Include Topology File (itp)</strong> of the parameterized ligand, including the parameters information: bonds, angles, dihedrals, etc.</li>
 </ul>