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List of miscellaneous tools MCCE offers for your research and convenience. Most of these tools support "-h" flags for additional information and use cases. Some of these tools are intended for pre-run analysis, and some are intended for post-run analysis. Pre...

Microstates are 

All MCCE tools relevant to microstate analysis will start with "ms", like 'ms_top2pdbs" and "ms_hbond_percentages.py".  To use any microstate tools, MCCE needs to have the directory "ms_out", produced by "step4.py --ms". Read the steps 1 - 4 tutorial for more...

MCCE offers a wide range of customizable parameter that influence the accuracy of its pKa predictions. Some major options include varying the internal dielectric constants, numerical Poisson-Boltzmann solvers, Van der Waal functions, conformer sampling level, ...

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.pd...

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 li...

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...