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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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Step-by-Step Output

Program start and Initialization

Input files:

  • run.prm: mcce control file
  • 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 
  • 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: 

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 - 

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. 

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. 

param - How 

pK.out (Output) - Sampling across different pHs 

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 - 

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