Tools and information for AMBER and CPPTRAJ examples
Posted: April 6, 2022
Evaluate the given mathematical expression. clear [{all | <type>}] (<type> = actions,trajin,trajout,ref,parm,analysis,datafile,dataset) Clear list of indicated type, or all lists if ‘all’ specified. Note that when clearing actions or analyses, associated data sets and data les are not… Read More
Category: CPPTRAJ, General Commands
Posted: April 6, 2022
Prevent Actions from writing in format information to STDOUT.
Category: CPPTRAJ, General Commands
Updated: April 6, 2022
Turn caching of data sets to disk on or off. usediskcache {on|off} If on, CPPTRAJ will attempt to cache data sets to disk if possible. This currently only works for integer data sets (e.g. hbond series data sets,… Read More
Category: CPPTRAJ, General Commands
Updated: April 6, 2022
Sort data sets using replica information (currently constant pH only) sortensembledata <dset arg0> [<dset arg1> …] <dset arg0> [<dset arg1> …] Data set(s) to sort. Sort unsorted data sets. Currently only works for constant pH REMD data.
Category: CPPTRAJ, General Commands
Updated: May 31, 2022
Read data files in ensemble mode. readensembledata <filename> [filenames <additional files>] [<readdata args>] <lename> Lowest replica file name. filenames <additional files> Specified additional members of the ensemble. If not specified ensemble members will be search for using numerical… Read More
Category: CPPTRAJ, Trajectory File Commands
Updated: April 6, 2022
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>… Read More
Category: Analysis Commands, CPPTRAJ
Updated: September 12, 2024
Prepare a structure (usually loaded from a PDB) for processing with LEaP from Amber. prepareforleap crdset <coords set> [frame <#>] name <out coords set> [pdbout <pdbfile> [terbymol]] [leapunitname <unit>] [out <leap input file> [runleap… Read More
Category: CPPTRAJ, Data Sets and Data Files
Posted: April 5, 2022
Split molecules in a COORDS set into a trajectory. splitcoords <crd set> name <output set name> <crd set> COORDS set to split. name <output set name> Name of new set to create. Split trajectory specified by <crd set>… Read More
Category: CPPTRAJ, Data Sets and Data Files
Posted: April 5, 2022
Concatenate two or more COORDS sets. catcrd <crd1> <crd2> … name <name> <crdX> COORDS data sets to concatenate, specify 2 or more. name <name> New COORDS set name. Concatenate two or more COORDS data sets into a single… Read More
Category: Coordinates Data Set commands, CPPTRAJ
Updated: April 5, 2022
Print improper info for selected atoms. improperinfo [parm <name> | parmindex <#> | <#>] [<mask1>] [<mask2> <mask3> <mask4>] [out <file>] [parm <name> | parmindex <#> | <#>] Name/tag or index of topology. Default is first loaded topology. [<mask1>]… Read More
Category: CPPTRAJ, Topology File Commands
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