Custom MCCE Runs and submit_shell

Default MCCE runs (run_mcce4)

By default, each step of MCCE has certain parameters set to it. For example, step 3 defaults to the Gunner Lab's in-house Poisson-Boltzmann solver, NGPB, though Delphi and ZAP are available to those with the respective OpenEye licenses. But what if the user wants non-default settings?

By default, run_mcce4 uses the following settings:

step1.py {input_pdb} -d 4 --dry
step2.py -l 1 -d 4
step3.py -d 4
step4.py --xts -i 7 -n 1

Each of these lines is a shell command. If you were to copy and paste these lines (after changing {input_pdb} to a local PDB file), MCCE would run just as though "run_mcce4" had been the command. To see more of our options, let's look at the output of "step1.py -h":

step1.py -h
usage: step1.py [-h] [--norun] [--noter] [-e /path/to/mcce] [-u Key=Value] [-d epsilon] [-load_runprm prm_file] [--dry] pdb

Run mcce step 1, premcce to format PDB file to MCCE PDB format.

positional arguments:
  pdb

options:
  -h, --help            show this help message and exit
  --norun               Create run.prm but do not run step 1; default: False.
  --noter               Do not label terminal residues (for making ftpl); default: False.
  -e /path/to/mcce      mcce executable location; default: mcce.
  -u Key=Value          User customized variables; default: .
  -d epsilon            protein dielectric constant for PBE solvers; default: 4.0.
  -load_runprm prm_file
                        Load additional run.prm file, overwrite default values.
  --dry                 Delete all water molecules; default: False.

So, if we wanted to start step 1 with an alternate version of MCCE, a dielectric constant of 8, and keeping explicit water molecules, we could change the command to:

step1.py {input_file.pdb} -e /home/other_mcce -d 8

Following a similar process for each step, we can create a full custom run to our liking.

submit_mcce4.sh

However, it's tedious to submit these instructions over and over. In MCCE4-Alpha/schedulers, a file named "submit_mcce4.sh" can be found. We recommend copying "submit_mcce4.sh" to the local directory and customizing it to fit the desired job. Let's look at the script:

# Input and Output:
input_pdb="prot.pdb"    # (INPDB)

# Set MCCE4 Parameters
MCCE_HOME="/home/MCCE4-Alpha"
USER_PARAM="./user_param"
EXTRA="./user_param/extra.tpl"
TMP="/tmp"
CPUS=1

# Step control flags
step1="t"               # STEP1: pre-run, pdb-> mcce pdb  (DO_PREMCCE)
step2="t"               # STEP2: make rotamers            (DO_ROTAMERS)
step3="t"               # STEP3: Energy calculations      (DO_ENERGY)
step4="t"               # STEP4: Monte Carlo Sampling     (DO_MONTE)
step_clean="t"          # Clean PBE data                  (BACKUP CLEAN) : Set to f if step3 --debug option is used

# Optional step controls
stepM="f"               # Generate Partial Membranes                    : If true, user MUST satisfy condidtions of stepM.sh, which can be be obtained on MCCE4/inhouse/stepM.sh
stepA="f"               # Run a custom script between step1 and step2   : If true, user MUST satisfy condidtions of their custom script
stepB="f"               # Run a custom script between step2 and step3   : If true, user MUST satisfy condidtions of their custom script
stepC="f"               # Run a custom script between step3 and step4   : If true, user MUST satisfy condidtions of their custom script

# MCCE Simulation
STEP1="step1.py -d 4 --dry"
STEP2="step2.py -d 4 -l 1"
STEP3="step3.py -d 4 -s delphi -p $CPUS -t \$TMP"
STEP4="step4.py --xts -i 7 -n 1"

# Optional MCCE script locations
STEPM="/path/to/stepM.sh"         # Optional StepM: Bash script
STEPA="/path/to/stepA_script.py"  # Optional StepA: Python script to run between step1 and step2.
STEPB="/path/to/stepB_script.py"  # Optional StepB: Python script to run between step2 and step3.
STEPC="/path/to/stepC_script.py"  # Optional StepC: Python script to run between step3 and step4.

# NOTE: User is responsible to precheck if custom scripts work properly and efficiently

"Set MCCE4 Parameters" controls which version of MCCE is being used.
"Step control flags" allow for steps to be turned on and off between runs.
"Optional step controls" allow for custom scripts to be run between steps, and partial membrane generation
"MCCE Simulation" is where each step is customized- use "step[1-4].py -h" to see options for each step
Lastly, the paths to any custom scripts are referenced

Then, submit_mcce4.sh can be executed:

chmod +x submit_mcce4.sh # make this file an executable
./submit_mcce4.sh # execute the submit shell