# MCCE Output Files
As part of the standard four steps, MCCE produces a number of files associated with the initial protein output. These are best understood to be members of six categories:
**Input:** The given PDB file. Often, MCCE programs will symbolically link the name "prot.pdb" to the input PDB file.
**Output:** Results of MCCE computation, to be interpreted by the user.
**Records:** Preserved information about the run.
**Instructions**: Files that control how MCCE runs. run.prm
**Control:** "Midpoint" files to preserve information between steps.
**Progress:** Benchmark files to keep track of what processes are occurring, and whether the run is succeeding.
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Most of these files will not need to be referenced to obtain pKa information. The most important files will be **bolded.** These files are input for the next step, or are the target output.
### Step-by-Step Output
#### Program start and Initialization
Input files:
- run.prm: mcce control file (if not specified, a default version from MCCE will be used)
- param: parameter directory (specified in run.prm)
- extra.tpl: extra parameters. Often used to correct for bias. (optional, specified in run.prm)
- new.tpl: temporary parameter file for unrecognized cofactors. (optional, created by step 1 if unknown residues are present)
#### Step 1: Formatting PDB File
Input files:
- **PDB file**
- name.txt: Rules for renaming/formatting residues and atoms.
- list\_rot.gold (still?)
Output files:
- acc.res: solvent accessibility of residues
- acc.atm: solvent accessibility of atoms
- new.tpl: parameter file template of unrecognized cofactors (not always created)
- head1.lst: summary of rotamer making policy of residues (optionally used by step 2? how does that work?)
- **step1\_out.pdb** (used by step 2):
#### Step 2: Making Rotamers
Input files:
- **step1\_out.pdb**: input structure of step 2 in mcce extended PDB format
- head1.lst: rotamer making policy of residues
Output files:
- progress.log: progress report file. Dynamically updated
- rot\_stat: rotamer making statistics, dynamically updated
- head2.lst: summary of rotamers made in step 2 (optionally used by step 3)
- **step2\_out.pdb**: step 2 output file with multiple rotamers in extended PDB format
#### Step 3: Calculate the Energy Lookup Table
Input files:
- **step2\_out.pdb**: Input instructions of step 3 in MCCE extended PDB format
Output files:
- progress.log: progress report file. Dynamically updated
- progress\_step3.log: logs specific conformers being processed. Used to estimate step 3 completion time.
- run.prm.record: Updates to keep track of settings- dielectric constant, solver, where MCCE is located, etc.
- **head3.lst**: rotamers in extended PDB format
- **energies** (directory): A collection of opp files, each one a pairwise interaction to a conformer.
#### Step 4: Monte Carlo pKa Titration
Input files:
- **head3.lst**: self-energy of conformers, Monte Carlo sampling flags of conformers
- **energies** (directory): energy lookup table for pairwise interaction between conformers
Output files:
- **pK.out**: pKa or Em values obtained by titration curve fitting
- sum\_crg.out: residue net charges
- fort.38: conformer occupancies- the pKa for each residue is extrapolated by where the occupancy is, or is predicted to be, .5.
#### Alphabetized List
acc.atm/acc.res (Control/Output) **-** Gives the percent surface accessibility to the solvent of the atom/residue. Used to make rotamers.
energies (Control) - Self and pairwise energies generated during step 3.
entropy.out **-** Table recording entropy for each conformer at different pH's.
err.log (Progress) **-** Similar to progress.log, terminal output is moved here in the event of an error. Usually empty.
fort.38 (Output) - The name is a reminder that MCCE's origins were in Fortran.
head1.lst/head2.lst/**head3.lst** (Control) **-** head1.lst is created by step 1, and can be modified to reduce the number of conformers made in step 2. head2.lst is a summary of rotamers made in step 2. head3.lst may be
- iConf:conformer ID
- CONFORMER: conformer name
- FL: flag| f means the conformer is on, t means the conformer is off.
- occ: occupancy
- crg: charge
- Em0: Em in solution
- pKa0: pka in solution
- ne: # of electrons
- nH: # of protons
- vdw0: self vdW energy + implicit vdW energy (favorable) with solvent (water)
mc\_out (Progress) **-** Provides details about the Monte Carlo process.
name.txt (Instructions) - The file referenced by mcce when renaming atom names, residue names, sequence number, and chain ID. The purpose is to unify residue names to 3-char MCCE names, and break some larger cofactors into smaller ones (e.g., extracting PAA from heme groups).
**param -** Contains necessary topology files, copied from the parent MCCE folder. If 00always\_needed.tpl or mcce.tpl have been changed after a successful run, the param folder acts as an archive for the topology files used at runtime.
**pK.out (Output) -** pKa or Em values obtained by titration curve fitting.
**prot.pdb (Input) -** The name MCCE often uses in reference to the original input file.
respair.lst **-** Records the pairwise energy for each pair of conformers.
rot\_stat (Progress) **-** Provides statistics about rotamer creation.
run.log (Record) **-** Keeps a record of terminal output from steps.
**run.prm (Instructions) -** Created by step 1 if not provided- grants extra control over MCCE settings. For example, by default, the pH titration occurs along whole numbers from 0 - 14. The TITR settings can be edited to reduce the range of the pH titration, increase the points of titration, and more.
run.prm.record **-** Records the full run.prm details for each step. **CAUTION: If different settings are used on different runs in the same direct, run.prm.record may not capture the changes to the settings.**
step0\_out.pdb**/step1\_out.pdb/step2\_out.pdb -** Restructured versions of the input file. step0\_out deletes any header information (e.g., the headers included in RCSB downloads of PDB files). step1\_out renames residues according to a file called name.txt, including the opening and concluding residues of a sequence to NTR and CTR, respectively. step2\_out.pdb expands the list to include alternative conformers as well.
sum\_crg.out **-** Records information about the net charge of the PDB's residues at each pH titration.
vdw0.lst **-** A conformer table that adds the energy from VDW interactions and the Interaction with Implicit Solvent (energy scaled by 0.06 kCal/mol/Angstrom^2), or SAS. Without the SAS term, the conformer is effectively in a vacuum.