Exercise #1: Sanity check using p_info

In this first exercise, we will introduce how to use basic pre-check tool called p_info on a real protein structure to confirm its compatibility with MCCE4. This exercise serves as a sanity check before running any pKₐ, Em, or microstate calculations.

We highly recommend to always run p_info on a new protein structure, since it allows you to:

  • Implore if the protein file contents are compatible for an MCCE4 simulation
  • Build intuition about what MCCE4 “sees” in your structure
  • Identify potential problems before performing expensive calculations
  • Recognize unsupported cofactors and nonstandard residue names
  • Decide whether new topology files or residue renaming are required

What does p_info do?

p_info performs an textual analysis of the input PDB file and reports it’s compatibility with MCCE4. By running p_info, you can quickly identify common issues that often prevent MCCE calculations from running correctly, such as formatting problems, missing atoms, or unsupported residues.

Specifically, p_info helps you:

✅ Verify that the PDB format is readable and compatible for an MCCE4 simulation

🔍 Identify recognized vs. unrecognized residues

🧪 Detect missing atoms, unusual naming conventions, or nonstandard residues

⚡ Check for charge-bearing residues relevant to pKₐ and Em calculations

💧 Summarize waters, ligands, and cofactors present in the structure

0. Pre-requisite:

Ensure you have the conda environment for mc4 activated.

conda activate mc4

1. Prepare the Inputs

Enter the working directory for the first exercise:

cd mcce_workflows
mkdir ex1; cd ex1

Download the PDB file for 1B2V:

getpdb 1b2v

A successful download should display the following message:

 [ INFO ] Download completed: 1b2v.pdb

2. Run p_info

p_info provides a count of amino acids by type and chain, ligand counts, and whether topology files are present for relevant ligands. p_info will run step 1 and create a file called “run1.log” as part of its functionality.

p_info 1b2v.pdb

3. Examine the screen output:

On a first run, the screen should display the following:

p_info requires 1b2v.pdb,its associated run1.log, and step1_out.pdbin the current directory.

Running step1.py...

Number of amino acids in the protein: 173
This is a small sized protein. It will run quickly.

Number of ligands in the protein: 4

We have topology files for these ligands:
TPLFOUND: {'PAA', '_CA', 'PDD', 'HEM'}

For more detailed analysis of the protein, look in p_info.log.