diff --git a/_posts/2023-10-27-Peptide-Docking-with-ADCP.md b/_posts/2023-10-27-Peptide-Docking-with-ADCP.md index e8f8c0d62e..da9080f330 100644 --- a/_posts/2023-10-27-Peptide-Docking-with-ADCP.md +++ b/_posts/2023-10-27-Peptide-Docking-with-ADCP.md @@ -34,7 +34,7 @@ To reproduce the presented work, you must have the software dependencies: * [Step 3: Local Optimization with Vina](#step-3-local-optimization-with-vina) + [Rigid Receptor Local Optimization](#rigid-receptor-local-optimization) + [Compare with Docking in Vina](#compare-with-docking-in-vina) - + [Flexible Receptor Local Optimization] + + [Flexible Receptor Local Optimization](#flexible-receptor-local-optimization) ## Step 1: Docking Calculation with ADCP @@ -305,7 +305,7 @@ mk_prepare_receptor.py \ `mk_prepare_receptor.py` does not tolerate missing and/or incomplete capping groups, so it won't work for `complex_1H_rec.pdb`. -The peptide ligand preparation can be done from a PDB file, using [`prepare_peptide_ligand.py])(https://github.com/rwxayheee/prepare_peptide_ligand/blob/main/prepare_peptide_ligand.py) I propose to prepare peptide ligand PDBQT file from a PDB file - +The peptide ligand preparation can be done from a PDB file, using [prepare_peptide_ligand.py])(https://github.com/rwxayheee/prepare_peptide_ligand/blob/main/prepare_peptide_ligand.py) I propose to prepare peptide ligand PDBQT file from a PDB file - ```python from prepare_peptide_ligand import * @@ -419,3 +419,5 @@ While Vina's output mode#1 (purple) adopts a very interesting conformation, with ![adcp-vina-overlay](/assets/img/adcp-vina-overlay.jpg) +### Flexible Receptor Local Optimization +