Added links to structure & ligand

biobb_wf_protein-complex_md_setup/docs/source/tutorial.md

@@ -1,7 +1,7 @@
 # Protein Ligand Complex MD Setup tutorial using BioExcel Building Blocks (biobb)
 **Based on the official Gromacs tutorial:** [http://www.mdtutorials.com/gmx/complex/index.html](http://www.mdtutorials.com/gmx/complex/index.html)
 ***
-This tutorial aims to illustrate the process of **setting up a simulation system** containing a **protein in complex with a ligand**, step by step, using the **BioExcel Building Blocks library (biobb)**. The particular example used is the **T4 lysozyme** L99A/M102Q protein (PDB code 3HTB), in complex with the **2-propylphenol** small molecule (3-letter Code JZ4). 
+This tutorial aims to illustrate the process of **setting up a simulation system** containing a **protein in complex with a ligand**, step by step, using the **BioExcel Building Blocks library (biobb)**. The particular example used is the **T4 lysozyme** L99A/M102Q protein (PDB code 3HTB, [https://doi.org/10.2210/pdb3HTB/pdb](https://doi.org/10.2210/pdb3HTB/pdb)), in complex with the **2-propylphenol** small molecule (3-letter Code JZ4, [https://www.rcsb.org/ligand/JZ4](https://www.rcsb.org/ligand/JZ4)). 
 ***
 
 ## Settings
@@ -63,8 +63,8 @@ jupyter-notebook biobb_wf_protein-complex_md_setup/notebooks/biobb_Protein-Compl
 <a id="input"></a>
 ## Input parameters
 **Input parameters** needed:
- - **pdbCode**: PDB code of the protein-ligand complex structure (e.g. 3HTB)
- - **ligandCode**: Small molecule 3-letter code for the ligand structure (e.g. JZ4)
+ - **pdbCode**: PDB code of the protein-ligand complex structure (e.g. 3HTB, [https://doi.org/10.2210/pdb3HTB/pdb](https://doi.org/10.2210/pdb3HTB/pdb))
+ - **ligandCode**: Small molecule 3-letter code for the ligand structure (e.g. JZ4, [https://www.rcsb.org/ligand/JZ4](https://www.rcsb.org/ligand/JZ4))
  - **mol_charge**: Charge of the small molecule, needed to add hydrogen atoms.
 
 

biobb_wf_protein-complex_md_setup/html/biobb_Protein-Complex_MDsetup_tutorial.web.html

@@ -13972,7 +13972,7 @@
 <div class="jp-Cell-inputWrapper"><div class="jp-InputPrompt jp-InputArea-prompt">
 </div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput " data-mime-type="text/markdown">
 <h1 id="Protein-Ligand-Complex-MD-Setup-tutorial-using-BioExcel-Building-Blocks-(biobb)">Protein Ligand Complex MD Setup tutorial using BioExcel Building Blocks (biobb)<a class="anchor-link" href="#Protein-Ligand-Complex-MD-Setup-tutorial-using-BioExcel-Building-Blocks-(biobb)">&#182;</a></h1><h3 id="Based-on-the-official-Gromacs-tutorial:-http://www.mdtutorials.com/gmx/complex/index.html">Based on the official Gromacs tutorial: <a href="http://www.mdtutorials.com/gmx/complex/index.html">http://www.mdtutorials.com/gmx/complex/index.html</a><a class="anchor-link" href="#Based-on-the-official-Gromacs-tutorial:-http://www.mdtutorials.com/gmx/complex/index.html">&#182;</a></h3><hr>
-<p>This tutorial aims to illustrate the process of <strong>setting up a simulation system</strong> containing a <strong>protein in complex with a ligand</strong>, step by step, using the <strong>BioExcel Building Blocks library (biobb)</strong>. The particular example used is the <strong>T4 lysozyme</strong> L99A/M102Q protein (PDB code 3HTB), in complex with the <strong>2-propylphenol</strong> small molecule (3-letter Code JZ4).</p>
+<p>This tutorial aims to illustrate the process of <strong>setting up a simulation system</strong> containing a <strong>protein in complex with a ligand</strong>, step by step, using the <strong>BioExcel Building Blocks library (biobb)</strong>. The particular example used is the <strong>T4 lysozyme</strong> L99A/M102Q protein (PDB code 3HTB, <a href="https://doi.org/10.2210/pdb3HTB/pdb">https://doi.org/10.2210/pdb3HTB/pdb</a>), in complex with the <strong>2-propylphenol</strong> small molecule (3-letter Code JZ4, <a href="https://www.rcsb.org/ligand/JZ4">https://www.rcsb.org/ligand/JZ4</a>).</p>
 <hr>
 <p><strong>Biobb modules</strong> used:</p>
 <ul>
@@ -14032,8 +14032,8 @@ <h3 id="Pipeline-steps:">Pipeline steps:<a class="anchor-link" href="#Pipeline-s
 <p><a id="input"></a></p>
 <h2 id="Input-parameters">Input parameters<a class="anchor-link" href="#Input-parameters">&#182;</a></h2><p><strong>Input parameters</strong> needed:</p>
 <ul>
-<li><strong>pdbCode</strong>: PDB code of the protein-ligand complex structure (e.g. 3HTB)</li>
-<li><strong>ligandCode</strong>: Small molecule 3-letter code for the ligand structure (e.g. JZ4)</li>
+<li><strong>pdbCode</strong>: PDB code of the protein-ligand complex structure (e.g. 3HTB, <a href="https://doi.org/10.2210/pdb3HTB/pdb">https://doi.org/10.2210/pdb3HTB/pdb</a>)</li>
+<li><strong>ligandCode</strong>: Small molecule 3-letter code for the ligand structure (e.g. JZ4, <a href="https://www.rcsb.org/ligand/JZ4">https://www.rcsb.org/ligand/JZ4</a>)</li>
 <li><strong>mol_charge</strong>: Charge of the small molecule, needed to add hydrogen atoms.</li>
 </ul>
 

biobb_wf_protein-complex_md_setup/notebooks/biobb_Protein-Complex_MDsetup_tutorial.ipynb

@@ -7,7 +7,7 @@
     "# Protein Ligand Complex MD Setup tutorial using BioExcel Building Blocks (biobb)\n",
     "### Based on the official Gromacs tutorial: http://www.mdtutorials.com/gmx/complex/index.html\n",
     "***\n",
-    "This tutorial aims to illustrate the process of **setting up a simulation system** containing a **protein in complex with a ligand**, step by step, using the **BioExcel Building Blocks library (biobb)**. The particular example used is the **T4 lysozyme** L99A/M102Q protein (PDB code 3HTB), in complex with the **2-propylphenol** small molecule (3-letter Code JZ4). \n",
+    "This tutorial aims to illustrate the process of **setting up a simulation system** containing a **protein in complex with a ligand**, step by step, using the **BioExcel Building Blocks library (biobb)**. The particular example used is the **T4 lysozyme** L99A/M102Q protein (PDB code 3HTB, [https://doi.org/10.2210/pdb3HTB/pdb](https://doi.org/10.2210/pdb3HTB/pdb)), in complex with the **2-propylphenol** small molecule (3-letter Code JZ4, [https://www.rcsb.org/ligand/JZ4](https://www.rcsb.org/ligand/JZ4)). \n",
     "***\n",
     "**Biobb modules** used:\n",
     "\n",
@@ -70,8 +70,8 @@
     "<a id=\"input\"></a>\n",
     "## Input parameters\n",
     "**Input parameters** needed:\n",
-    " - **pdbCode**: PDB code of the protein-ligand complex structure (e.g. 3HTB)\n",
-    " - **ligandCode**: Small molecule 3-letter code for the ligand structure (e.g. JZ4)\n",
+    " - **pdbCode**: PDB code of the protein-ligand complex structure (e.g. 3HTB, [https://doi.org/10.2210/pdb3HTB/pdb](https://doi.org/10.2210/pdb3HTB/pdb))\n",
+    " - **ligandCode**: Small molecule 3-letter code for the ligand structure (e.g. JZ4, [https://www.rcsb.org/ligand/JZ4](https://www.rcsb.org/ligand/JZ4))\n",
     " - **mol_charge**: Charge of the small molecule, needed to add hydrogen atoms."
    ]
   },