Tools and information for AMBER and CPPTRAJ examples
Updated: March 27, 2019
Run an analysis immediately or run all queued analyses runanalysis [<analysiscmd> [<analysis args>]] Run given analysis command immediately and write any data generated. If no command is given run any analysis currently set up. NOTE: When ’runanalysis’ is… Read More
Updated: April 12, 2023
Read data sets from files. readdata <filename> [name <dsname>] [as <fmt>] [separate] … Read More
Updated: March 28, 2019
Parameter and reference files may be ’tagged’ (i.e. given a nickname). These tags can then be used in place of the file name itself. A tag in cpptraj is recognized by being bounded by brackets (’[’ and ’]’)…. Read More
Posted: February 20, 2019
Ranges instead of atom masks. For several commands some arguments are ranges (e.g. ’trajout onlyframes <range>’, ’nastruct resrange<range>’, ’rmsd perres range <range>’); THESE ARE NOT ATOM MASKS. They are simple number ranges using ’-’ to specify a range… Read More
Updated: January 26, 2024
The mask syntax is similar to PTRAJ. Note that the characters ’:’, ’@’, and ’*’ are reserved for masks and should not be used in output file or data set names. All masks are case-sensitive. Either names or… Read More
Updated: February 20, 2019
Cpptraj uses the AKMA system of units. The exception is time, which is typically expressed in ps (except where noted). Variable Unit Length Angstrom Energy kcal/mol Mass AMU Charge electron Time ps (typically) Force kcal/mol*Angstrom
Updated: November 4, 2021
Like ptraj, a trajectory processing “Run” is one of the main ways to run cpptraj. First the Run is set up via commands read in from an input file or the interactive prompt. Trajectories are then read… Read More
Posted: February 20, 2019
In “interactive mode” users can enter commands in a UNIX-like shell. Interactive mode is useful for running short and simple analyses or for trying out new kinds of analyses. If cpptraj is run with ’–interactive’, no arguments, or… Read More
Posted: February 20, 2019
In “batch” mode, cpptraj is executed from the command line with one or more input files containing commands to be processed or STDIN. The syntax of <input file> is similar to that of ptraj. Keywords specifying different commands… Read More
Updated: November 4, 2021
Input to CPPTRAJ is in the form of commands, which can be categorized in to 2 types: immediate and queued. Immediate commands are executed as soon as they are encountered. Queued commands are initialized when they are… Read More
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