Fixed outputs tutorial

biobb_wf_amber/html/md_setup_lig/biobb_wf_amber_md_setup_lig.web.html

@@ -9915,16 +9915,16 @@ <h3 id="Step-2:-Visualizing-the-generated-dehydrated-trajectory.">Step 2: Visual
 <p><a id="output"></a></p>
 <h2 id="Output-files">Output files<a class="anchor-link" href="#Output-files">¶</a></h2><p>Important <strong>Output files</strong> generated:</p>
 <ul>
-<li>output_ions_pdb_path (structure.ions.pdb): <strong>System structure</strong> of the MD setup protocol. Structure generated during the MD setup and used in the MD simulation. With hydrogen atoms, solvent box and counterions.  </li>
-<li>output_free_traj_path (sander.free.netcdf): <strong>Final trajectory</strong> of the MD setup protocol.</li>
-<li>output_free_rst_path (sander.free.rst): <strong>Final checkpoint file</strong>, with information about the state of the simulation. It can be used to <strong>restart</strong> or <strong>continue</strong> a MD simulation.</li>
-<li>output_ions_top_path (structure.ions.parmtop): <strong>Final topology</strong> of the MD system in AMBER Parm7 format.</li>
+<li><strong>output_ions_pdb_path</strong> (structure.ions.pdb): <strong>System structure</strong> of the MD setup protocol. Structure generated during the MD setup and used in the MD simulation. With hydrogen atoms, solvent box and counterions.  </li>
+<li><strong>output_free_traj_path</strong> (sander.free.netcdf): <strong>Final trajectory</strong> of the MD setup protocol.</li>
+<li><strong>output_free_rst_path</strong> (sander.free.rst): <strong>Final checkpoint file</strong>, with information about the state of the simulation. It can be used to <strong>restart</strong> or <strong>continue</strong> a MD simulation.</li>
+<li><strong>output_ions_top_path</strong> (structure.ions.parmtop): <strong>Final topology</strong> of the MD system in AMBER Parm7 format.</li>
 </ul>
 <p><strong>Analysis</strong> (MD setup check) output files generated:</p>
 <ul>
-<li>output_rms_first (3htb_rms_first.dat): <strong>Root Mean Square deviation (RMSd)</strong> against <strong>minimized and equilibrated structure</strong> of the final <strong>free MD run step</strong>.</li>
-<li>output_rms_exp (3htb_rms_exp.dat): <strong>Root Mean Square deviation (RMSd)</strong> against <strong>experimental structure</strong> of the final <strong>free MD run step</strong>.</li>
-<li>output_rgyr (3htb_rgyr.dat): <strong>Radius of Gyration</strong> of the final <strong>free MD run step</strong> of the <strong>setup pipeline</strong>.</li>
+<li><strong>output_rms_first</strong> (3htb_rms_first.dat): <strong>Root Mean Square deviation (RMSd)</strong> against <strong>minimized and equilibrated structure</strong> of the final <strong>free MD run step</strong>.</li>
+<li><strong>output_rms_exp</strong> (3htb_rms_exp.dat): <strong>Root Mean Square deviation (RMSd)</strong> against <strong>experimental structure</strong> of the final <strong>free MD run step</strong>.</li>
+<li><strong>output_rgyr</strong> (3htb_rgyr.dat): <strong>Radius of Gyration</strong> of the final <strong>free MD run step</strong> of the <strong>setup pipeline</strong>.</li>
 </ul>
 </div>
 </div>