# p_batch tutorial # Multiple PDB MCCE Runs (pro_batch) p_batch is a program included in MCCE, under the folder MCCE_bin. It accepts a directory containing ".pdb" files, and runs MCCE with identical settings on each protein file. Usage: p_batch protein_dir [custom_script.sh] By default, default_script.sh is created by p_batch at run time, if it does not exist. The default scripts calls for steps 1-4 of MCCE to be run at level 1, assumes a dielectric constant of 8 with NGPB as the Poisson Bolztmann solver, and sets entropy control on. Another tool is available called "pro_batch". This behaves very similarly to p_batch, though the file pro_batch creates by default has more features for heavy users. # 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](https://vdiflorio.github.io/nextgenpb_tutorial/), 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: ```bash chmod +x submit_mcce4.sh # make this file an executable ./submit_mcce4.sh # execute the submit shell ``` We recommend using custom submit shells in conjunction with p\_batch/pro\_batch. These programs included with MCCE4-Alpha are able to accept a -custom flag and a local shell script, to execute it across all relevant jobs. [Learn about this functionality here](https://mccewiki.levich.net/books/p-batch-tutorial/page/how-do-i-run-multiple-proteins-at-once-p-batch-and-pro-batch). # How do I run multiple proteins at once? p_batch and pro_batch p\_batch is a program included in MCCE, under the folder MCCE\_bin. It accepts a directory containing ".pdb" files, and runs MCCE with identical settings on each protein file. ``` p_batch -h usage: p_batch [-h] [-custom script_path] input_path p_batch accepts a directory containing PDB files, and executes identical MCCE runs in directories named after each respective PDB file. positional arguments: input_path Path to a .pdb file options: -h, --help show this help message and exit -custom script_path Give a shell script with custom instructions. If not defined, a default script will be created and used. ``` By default, default\_script.sh is created by p\_batch at run time, if it does not exist. The default scripts calls for steps 1-4 of MCCE to be run at level 1, assumes a dielectric constant of 8 with NGPB as the Poisson Bolztmann solver, and sets entropy control on. Another tool called "pro\_batch" is available. This behaves very similarly to p\_batch, though the default instruction script pro\_batch creates has more features for heavy users, including the ability to use a scheduler. Both p\_batch and pro\_batch can accept custom shell scripts with the "-custom" flag. [Learn about creating and editing shell scripts here.](https://mccewiki.levich.net/books/p-batch-tutorial/page/custom-mcce-runs-and-submit-shell) ``` pro_batch -h usage: pro_batch [-h] [-custom script_path] [--sbatch | --no-sbatch] input_path pro_batch accepts a directory containing PDB files, and executes identical MCCE runs in directories named after each respective PDB file. pro_batch creates a high-level shell script. The user then edits the shell script to their liking, and executes it with the -custom flag. positional arguments: input_path Path to a directory containing PDB files. options: -h, --help show this help message and exit -custom script_path Give a shell script with custom instructions. If not defined, a default script will be created and used. --sbatch, --no-sbatch Turn on this flag to use a scheduler. (default: False) ``` Let's look at an example of how p\_batch can be used. First, create a directory, and fill it with protein files. For this example, assume a directory called "source\_files" containing a couple PDB files. ``` user@example:/pro_batch_testing$ ls source_files 1ans.pdb 4pti.pdb ``` Now, let's use p\_batch. ``` p_batch source_files New book.txt created. You can remove protein files to be run by editing book.txt if desired, and resume by running p_batch again. These proteins will be run: 4pti 1ans Pre-existing directories for these proteins will be emptied and replaced with information from the new run. Run MCCE with the current settings? (yes/y/no) ``` Typing "yes" or "y" will start the default MCCE process in each directory (unless the -custom flag is used to choose an alternate script). ``` Processing source_files/4pti.pdb... Processing source_files/1ans.pdb... Bash script is being executed in each directory. Double check processes are running with command 'top', or 'mcce_stat'. mcce_stat also updates book.txt to reflect completed runs. ``` ### mcce\_stat Reviewing multiple protein runs can be cumbersome. To aid the user, "mcce\_stat" is included. The directories created by p\_batch or pro\_batch will contain the output files of each MCCE run. mcce\_stat checks of these directories for "signal" files to check how each run is progressing, as of mcce\_stat's runtime. ``` mcce_stat 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". ### book.txt Before beginning the MCCE run, the program creates a file named "book.txt". book.txt is a text file containing a list names of proteins that can be edited to "turn off" proteins. This is what our new book.txt file looks like: ```bash 4pti 1ans ``` If we wanted to turn off both of these, we could edit book.txt to: ``` 4pti x 1ans c ``` Where "x" means exclusion, and "c" means completed. Attempting to run p\_batch now results in the following message: ``` p_batch source_files/ book.txt found! Protein files identified in book.txt: 4pti x 1ans c No runnable proteins found. Remove 'c' or 'x' from lines in book.txt to make them runnable, add protein files to run, or delete book.txt to re-do all runs. Aborting MCCE... ``` In this way, the user can choose any desired subset of proteins from the source directory's protein set.