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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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. 

mc_out (Progress) - Provides details about the Monte Carlo process.

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 -