MCCE Multiple PDB runs

The pro_batch utility tool, located in MCCE_bin, automates MCCE4 runs across multiple PDB files. It creates individual directories for each protein and applies identical settings across the entire batch.

pro_batch -h

usage: pro_batch [-h] [-custom CUSTOM] [--sbatch] [--check] input_path

Batch launch MCCE runs.

positional arguments:
  input_path      Path to a directory containing PDB files.

options:
  -h, --help      show this help message and exit
  -custom CUSTOM  Path to custom bash script.
  --sbatch        Run all jobs separately using the Slurm scheduler (sbatch).
  --check         Update book.txt status and exit.

By default, pro_batch creates a submit_mcce4.sh script if one is not already present in your working directory. The default configuration includes:

  • Conformer-Generatiion Level: Level 1
  • Dielectric Constant: 8
  • PB Solver: NGPB
  • Entropy Control: On

pro_batch can also accept custom shell scripts with the "-custom" flag. Learn about creating and editing shell scripts here.

1. Basic Usage Example

To run a batch, first organize your PDB files into a single directory. You can use getpdb (included in MCCE4-Alpha/MCCE_bin) to download files directly from RCSB. For this example, assume a directory called source_files containing a couple PDB files:

ls source_files

Output:

1ans.pdb  4lzt.pdb  4pti.pdb  9rat.pdb

Now, let’s use pro_batch.

pro_batch source_files

If it is your first time running pro_batch in a directory, pro_batch will pull the default script submit_mcce4.sh from your MCCE4-Alpha\schedulers folder with the message: Created default submit_mcce4.sh. Edit it then re-run.

Once the script exists, running the command again will launch the jobs:

Found 4 new or missing runs: 1ANS, 4LZT, 4PTI, 9RAT

Launching 4 runs...
  -> Starting 4lzt...
Submitted batch job 10674
  -> Starting 4pti...
Submitted batch job 10675
  -> Starting 9rat...
Submitted batch job 10676
  -> Starting 1ans...
Submitted batch job 10677

Done. Monitor status in book.txt.

2. Monitoring Your Runs

MCCE4 provides two primary tools to track your progress: book.txt and mcce_stat.

  1. Using book.txt

Let’s take a look at the book.txt file:

Last Updated: 2026-02-05 20:03:23
PDB          Status   Last_Step
--------------------------------------
1ANS         r        Pending
4LZT         r        Pending
4PTI         r        Pending
9RAT         r        Pending

--------------------------------------
Legend:
 r : Ready or Running
 c : Completed (pK.out found)
 e : Error (Check run.log in directory)

Refreshing book.txt

  • The book.txt file acts as a master ledger. However, it does not update automatically. To refresh the status of your runs, use the --check flag:
pro_batch source_files --check

Output: Book status refreshed in book.txt.

Now we see that 1ANS successfully completed, but the rest of proteins are still in the Step3 stage:

Last Updated: 2026-02-05 20:04:20
PDB          Status   Last_Step
--------------------------------------
1ANS         c        Completed
4LZT         r        In Step3
4PTI         r        In Step3
9RAT         r        In Step3

--------------------------------------
Legend:
 r : Ready or Running
 c : Completed (pK.out found)
 e : Error (Check run.log in directory)
  1. Using mcce_stat

For a more detailed view of which specific steps (1–4) are finished for each protein, run mcce_stat from your working directory:

mcce_stat

Output:

To see when PDB was run, reference mcce_timing.log in running directory. (pro_batch)

Completion: 7.50%
Directory step1         step2         step3     step4  Status
1ans      Exists        Exists                               
4pti      Exists

When all four steps are completed, the pKas of the selected protein will be available to see in “pK.out”.

3. Advanced Configuration: –sbatch and –custom

  1. Resource Management Part of using pro_batch is memory management. When using the --sbatch flag, pro_batch utilizes the SLURM scheduler. You can manage memory and CPU usage by editing the header of your submit_mcce4.sh file:
# Parameter/Options for SLURM (Simple Linux Utility for Resource Management)
#SBATCH --job-name=submit_mcce4
#SBATCH --output=submit_mcce4.log
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --mem=12G                 # Adjust memory if needed
#SBATCH --export=ALL

If additional resources are available, the “–mem” line can be edited to add the amount of memory dedicated. Tip: Use the lscpu command to gauge your system’s capacity. For large proteins, you can add the -p flag to Step 3 in your script to process conformers in parallel, significantly reducing > >run time.

  1. Using Custom Scripts If you require specific parameters (like different pH ranges or dielectric constants), use the -custom flag to point to your own shell script as an alternative to submit_mcce4.sh:
pro_batch source_files -custom my_analysis_settings.sh

We anticipate the default settings for pro_batch will meet most users’ needs, but the full power of pro_batch is realized with the -custom flag, which allows a custom shell script to be executed in each protein directory. Learn about the submit_shell here.