Calculate statistics for constant pH data sets.

cphstats <pH sets> [name <name>] [statsout <statsfile>] [deprot] [fracplot [fracplotout <file>]]

<pH sets> Previously read in pH data sets.
name <name> Output set name.
statsout <statsle> Write pH statistics to <statsfile>
deprot If specified, calculate fraction deprotonated instead of protonated.
fracplot If specified, calculate fraction protonated/deprotonated vs pH.
fracplotout <le> File to write fraction plots to.

Data Sets Generated:
<name>[Frac]:<idx> Fraction protonated/deprotonated for residue <idx>.

Calculate statistics for constant pH simulation data previously read in with readdata. Statistics are calculated for each residue at each input pH. Output format is as follows:

Solvent pH is <pH> 
<res name> <res num> : Offset <off> Pred <pred> Frac Prot <frac> Transitions <#trans> 
Average total molecular protonation: <avg>

Where <off> isosetfrom predicted, <pred> is predicted pH, and <#trans> is the number of transitions. A line is printed for each residue. This functionality is similar to the cphstats utility that comes with Amber.

Note that data from constant pH REMD must be sorted prior to use with cphstats. See the readensembledata and sortensembledata commands for more details. For example, to read in constant pH data from constant pH REMD, sort and analyze:

readensembledata ExplicitRemd/cpout.001 cpin ExplicitRemd/cpin name PH 
sortensembledata PH 
runanalysis cphstats PH[*] statsout stats.dat fracplot fracplotout frac.agr deprot