add on post link for downloadable files

rwxayheee · Nov 11, 2023 · d75a6d4 · d75a6d4
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diff --git a/_posts/2023-10-27-Peptide-Docking-with-ADCP.md b/_posts/2023-10-27-Peptide-Docking-with-ADCP.md
@@ -22,6 +22,18 @@ To reproduce the presented work, you must have the software dependencies:
 + [Meeko](https://github.com/forlilab/Meeko) (Python Bindings, v0.5)
 + [AutoDock Vina](https://github.com/ccsb-scripps/AutoDock-Vina) (Python Bindings, v1.2.5) 
 
+## Associated Files
+
+<a href="{{ site.url }}/files/peptide-docking.zip" download>peptide-docking.zip</a>
+
+Contains input PDB files, `2xpp_iws1.pdb` and `2xpp_FFEIF.pdb`, for the peptide docking examples. 
+
+```
+peptide-docking/
+├── 2xpp_FFEIF.pdb
+└── 2xpp_iws1.pdb
+```
+
 # Table of Contents
 
 * [Step 1: Docking Calculation with ADCP](#step-1-docking-calculation-with-adcp)

diff --git a/_posts/2023-11-8-Peptide-Docking-with-ADCP-2.md b/_posts/2023-11-8-Peptide-Docking-with-ADCP-2.md
@@ -17,6 +17,12 @@ The intent of the post is to introduce to our lab members the new features in AD
 
 This post includes our own examples of docking calculations for standard amino acid (AA) peptides, cyclic peptides and peptides with D-amino acids which have better support in ADCP v1.1. The post-processing in AutoDock Vina, which we used for ADCP v1.0, is compared with the new post-processing protocol in this post using the OpenMM funtionalities that were embedded in ADCP v1.1. Lastly, because the minimization is performed *in vacuo*, we want to recalculate the binding energy and free energy in Amber using an implicit solvation model. 
 
+## Associated Files
+
+<a href="{{ site.url }}/files/peptide-docking.zip" download>peptide-docking.zip</a>
+
+Contains input PDB files, `2xpp_iws1.pdb` and `2xpp_FFEIF.pdb`, for the peptide docking examples. 
+
 # Table of Contents
 
 * [Example 1-1: Docking a Standard AA, 5-mer Peptide and Using OpenMM for Minimization](#example-1-1-docking-a-standard-aa-5-mer-peptide-and-using-openmm-for-minimization)

diff --git a/menu/about.md b/menu/about.md
@@ -10,4 +10,10 @@ The **associated files** are placed under the `files` directory of this project.
 
 <a href="{{ site.url }}/files/peptide-docking.zip" download>peptide-docking.zip</a>
 
-Contains input PDB files, `2xpp_iws1.pdb` and `2xpp_FFEIF.pdb`, for the peptide docking examples. 
+Contains input PDB files, `2xpp_iws1.pdb` and `2xpp_FFEIF.pdb`, for the peptide docking examples. 
+
+```
+peptide-docking/
+├── 2xpp_FFEIF.pdb
+└── 2xpp_iws1.pdb
+```