Exercise #4: Single-pH Charge microstate (MS) analysis on 4LZT

In this exercise, we will run a custom simulation on 4LZT and process its microstates ensemble to produce ‘charge microstates’ for further analysis using MCCE4.

0. Pre-requisite:

Ensure you have the conda environment for mc4 activated.

conda activate mc4

Ensure you have installed MCCE4-Tools. If not, please follow these steps.

Verify availability

To verify the successful installation and check the availability of the ms_protonation program, run the following commands

 which MCCE4-Tools
 which ms_protonation

1. Prepare the directory

Enter the working directory for this exercise:

cd mcce_workflows
mkdir ex4; cd ex4

Download the PDB file for 4LZT:

 getpdb 4lzt

A successful download should display the following message:

[ INFO ] Download completed: 4lzt.pdb

We strongly recommend to run p_info to inspect an unfamiliar PDB file and verify if it is compatible with MCCE4.

p_info 4lzt.pdb

2. Run the Customized MCCE calculation

Because we require the microstate file, we must use the following custom command to run MCCE4.

run_mcce4 4lzt.pdb -initial 7 -interval 1 -n 1 --ms

–ms, enable microstate output, which is not written as an output file in the default MCCE4 run.

Confirm the output files

When the run completes, confirm that the file head3.lst and the directory /ms_out/pH7.00eH0.00ms.txt exist. That directory should have a single .txt file with a name starting with ‘pH7’; this file is often referred to as ‘the msout file’. These are required inputs for the microstate analysis program.

ls ms_out/

3. Run ms_protonation (a tool in MCCE4-Tools)

_Input Files (Required)

The following input files must be present in the working directory to run the program ms_protonation.

  • head3.lst from MCCE output

    • sum_crg.out from MCCE output

  • ms_out/pH7.00eH0.00ms.txt from MCCE output Microstate file

  • params.crgms Parameter file (To know more about the params.crgms file, please see here).

How to get the params.crgms file?

Required command line argument: The filepath of a parameter file with extension ‘.crgms’.
Obtain a parameter file copy in this directory by running these commands:

CLONE=$(dirname $(dirname "$(python3 -c "import os, sys; print(os.path.realpath(sys.argv[1]))" "$(which ms_protonation)")"));
echo "$CLONE";
cp $CLONE/mcce4_tools/tool_param/params.crgms .

For more help, run the following command: ms_protonation -h

Run the full command:
Once your parameter (.crgms) file is ready, run the following command to execute the program.

ms_protonation params.crgms

It will take a few minutes to complete.

Output directories The output directory name would be crgms_corr_pH7.00eH0.00. Run the following command to see the output files.

cd crgms_corr_pH7.00eH0.00/
ls -l

Data outputs: The following outputs will be in the output directory (To know more about the output files, please see here).

all_crg_count_resoi.csv
all_res_crg_status.csv
corr.png
crg_count_res_of_interest.csv
crgms_logcount.png
enthalpy_dist.png
fixed_res_of_interest.csv

If it produces, the correlation matrix figure, ‘corr.png’, will indicate correlations among residues.

Reference: