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 2ycc

A successful download should display the following message:

 [ INFO ] Download completed: 2ycc.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 2ycc.pdb

3. Examine the screen output:

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

p_info requires 2ycc.pdb, its associated run1.log, and step1_out.pdb in the current directory.

Running step1.py...

Number of amino acids in the protein: 107
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: {'PDD', 'HEM', 'PAA'}

We do not have topology files for these ligands:
NOTPL: ['M3L']

For ligands with no topology files, here are your options:
        (1) Continue as is: These ligands will be treated as hydrophobic groups, with zero charge and zero vdw in new.tpl.
        (2) Repeat step1 with ligands removed: Remove ligands from input pdb and redo step1.
        (3) Repeat step1 after creating topology files for ligands. For instructions on creating topology files, go to:
            https://gunnerlab.github.io/mcce4_tutorial/docs/topology/

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

p_info provides amino acid counts and ligand counts. p_info also provides information on which ligands have topology files and which don’t. Certain ligands may look different or new ligands may appear in these lists as MCCE4 can modify or break up ligands to better process them. In this example, HEM is a ligand in 2ycc.pdb. However, it is broken into 2 ligands, PDD and PAA. Information is also provided on how to deal with ligands with no topology files. For more information on topology files, go to: Create MCCE4 Topology Files.

4. Examine the p_info log file

In order to get a more in-depth analysis of the protein, look in the p-info log file. Display the p_info log file:

cat p_info.log

The screen should display the following:

p_info requires 2ycc.pdb, its associated run1.log, and step1_out.pdb in the current directory.

Running step1.py...

p_info by Jared Suchomel, with contributions by Marilyn Gunner, Cat Chenal, and Junjun Mao! It's still in progress!

### For the input 2ycc.pdb:

Amino Acid Counts (of 107 Total):
Ionizable           Polar               Hydrophobic
---------------------------------------------------
LYS: 15             THR: 9              GLY: 12
GLU: 7              ASN: 7              LEU: 8
HIS: 4              TYR: 5              ALA: 7
ASP: 4              SER: 4              PHE: 4
ARG: 3              CYS: 2              PRO: 4
                    GLN: 2              ILE: 4
                                        VAL: 3
                                        MET: 2
                                        TRP: 1
---------------------------------------------------
Total: 33         Total: 29           Total: 45

Total           PDB Count     MCCE Count     Difference
Amino Acids     107           107            0
Ligands         3             4              1
Waters          61            6              55

### The PDB file has 1 chain(s).

This is a small sized protein. It will run quickly.

Waters and ions stripped if 5% of their Surface Area is exposed to Solvent.

SAS exposure limit edited in 'run.prm' parameter (H2O_SASCUTOFF).

Groups that can be deleted listed in 00always_needed.tpl.

NOTE: By default, waters are retained for an 'explicit solvent' run. Use the '--dry' flag for an 'implicit solvent' run.

These residues have been modified:

### TERMINI:

      Labeling "THR A  -5" as NTR
      Labeling "GLU A 103" as CTR

0 missing atoms added. This number DOES NOT include atoms relabeled as NTR, or CTR. See run1.log for full list.
53 atoms changed.

### LIGANDS:


      Ligand counts for chain A, in step1_out.pdb:
          PAA: 1
          M3L: 1
          PDD: 1
          HEM: 1

      Distance below bond threshold, renaming amino acid CYS A 14   to ligand CYL
      Distance below bond threshold, renaming amino acid CYS A 17   to ligand CYL
      Distance below bond threshold, renaming amino acid HIS A 18   to ligand HIL
      Distance below bond threshold, renaming amino acid MET A 80   to ligand MEL

      Groups are renamed or deleted relative to the input protein.

The rules for changes, and examples:

      FE   HEC A 104 -> FE   HEM A 104
       CAA HEM A 104 ->  CAA PAA A 104
       CAD HEM A 104 ->  CAD PDD A 104

A list of all atoms that are modified can be found in run1.log.

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

We do not have topology files for these ligands:
      NOTPL: ['M3L']

For ligands with no topology files, here are your options:
        (1) Continue as is: These ligands will be treated as hydrophobic groups, with zero charge and zero vdw in new.tpl.
        (2) Repeat step1 with ligands removed: Remove ligands from input pdb and redo step1.
        (3) Repeat step1 after creating topology files for ligands. For instructions on creating topology files, go to:
            https://gunnerlab.github.io/mcce4_tutorial/docs/topology/

p_info was run at local time Fri Jan 23 2026, 11:52AM

Thanks for using p_info! It's free!

Exercise #1: Sanity check using p_info

What does p_info do?

Specifically, p_info helps you: