typo in old post

_posts/2023-10-27-Peptide-Docking-with-ADCP.md

@@ -48,7 +48,7 @@ Following the steps in the [ADCP documentation](https://ccsb.scripps.edu/adcp/tu
 reduce 2xpp_iws1.pdb > 2xpp_recH.pdb;
 ```
 
-It should be noted that reduce will not protonate any of the imidazole nitrogens on HIS sidechains, unless with option `-NOFLILP` (or `-HIS` or `-BUILD`). 
+It should be noted that reduce will not protonate any of the imidazole nitrogens on HIS sidechains, unless with option `-NOFLIP` (or `-HIS` or `-BUILD`). 
 
 ```s
 reduce 2xpp_FFEIF.pdb > 2xpp_pepH.pdb;

_posts/2023-11-8-Peptide-Docking-with-ADCP-2.md

@@ -11,20 +11,24 @@ image: coming-soon.jpg
 
 This post is based on some basic knowledge and familarity with **peptide docking** using [Autodock CrankPep (ADCP)](https://ccsb.scripps.edu/adcp), as described in the [previous post](https://rwxayheee.github.io/Peptide-Docking-with-ADCP). 
 
-The intent of the post is to introduce *to our lab members* the new features in ADCP v1.1, including the most useful **OpenMM minimization** and the incorporation of nonstandard residues, followed by some additional steps that might benefit our own work such as **parsing and exporting the output to RDKit** for post-processing, and finally **to Amber for the MM/GBSA calculation**. 
+The intent of the post is to introduce to our lab members the new features in ADCP v1.1, including the most useful **OpenMM minimization** and the incorporation of D-amino acids, followed by some additional steps that might benefit our own work such as **parsing and exporting the output to RDKit** for post-processing, and finally **to Amber for the MM/GBSA calculation**. 
 
 # Overview
 
-This post includes our own examples of docking calculations for standard AA peptides, cyclic peptides and peptides with D-amino acids which have better support in ADCP v 1.1. 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. 
+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. 
 
 # 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](#example-1-1-docking-a-standard-aa-5-mer-peptide-and-using-openmm-for-minimization)
 * [Example 1-2: Exporting Parameters and Coordinates from OpenMM into Amber for MM/GBSA Calculation]
 
 * [Example 2-1: Docking a Standard AA, 5-mer Peptide and Using Vina for Local Optimization]
 * [Example 2-2: Exporting Molecules from RDKit into Amber for MM/GBSA Calculation]
 
-* [Example 3: Docking a cyclice peptide containing a Disulfide Bond and Pose Selection]
+* [Example 3: Docking a Cyclice Peptide Containing a Disulfide Bond and Pose Selection]
 
-* [Example 4: Docking a peptide containing D-amino acids and Backbone Dihedral Validation]
+* [Example 4: Docking a Peptide Containing D-Amino Acids and Backbone Dihedral Validation]
+
+## Example 1-1: Docking a Standard AA, 5-mer Peptide and Using OpenMM for Minimization
+
+The preparation steps for the docking calculation can be performed the same way as described in section [Structure and Target Preparation](https://rwxayheee.github.io/Peptide-Docking-with-ADCP#structure-and-target-preparation) in the previous post.