Tools and information for AMBER and CPPTRAJ examples
Updated: November 18, 2023
Many analysis commands can be used to analyze multiple data sets. The general format for selecting data sets is: <name>[<aspect>]:<index> The ’*’ character can be used as a wild-card for entire names (no partial matches). <name>: The data… Read More
Updated: August 31, 2023
Combine two or more COORDS sets combinecrd <crd1> <crd2> … [parmname <topname>] [crdname <crdname>] <crdX> COORDS data set to combine, specify 2 or more. [parmname <topname>] Name of combined Topology. [crdname <crdname>] Name of combined COORDS data set…. Read More
Updated: February 26, 2020
Run a single Action on a COORDS set. crdaction <crd set> <actioncmd> [<action args>] [crdframes <start>,<stop>,<offset>] Perform action <actioncmd> on COORDS data set <crd set>. A subset of frames in the COORDS data set can be specified with… Read More
Updated: April 5, 2022
Write a COORDS set to a file crdout <crd set> <filename> [<trajout args>] [crdframes <start>,<stop>,<offset>] Write COORDS data set <crd set> to trajectory named <filename>. A subset of frames in the COORDS data set can be specified with… Read More
Updated: March 27, 2019
Create a COORDS set during a run This command is actually an Action that can be used to create COORDS data sets during trajectory processing, see the createcrd command.
Updated: December 1, 2022
Create or append to a COORDS set from a file loadcrd <filename> [parm <parm> | parmindex<#>] [<trajin args>] [name <name>] [prec {single|double} <filename> Trajectory file to load. [parm <parmle/tag>] Topology filename/tag to associate with trajectory (default first topology)…. Read More
Updated: April 5, 2022
Create special COORDS set where frames remain on disk loadtraj name <setname> [<filename>] This command functions in two ways. If <filename> is not provided, all currently loaded input trajectories (from trajin commands) are added to TRAJ data set… Read More
Updated: March 27, 2019
Rotate specified dihedral(s) in given COORDS set by specific interval or to random values permutedihedrals crdset <COORDS set> resrange <range> [{interval | random}] [outtraj <filename> [<outfmt>]] [crdout <output COORDS>] [<dihedral types>] Options for ’random’: [rseed <rseed>] [out <#… Read More
Updated: March 27, 2019
Rotate specified dihedral to specified value or by given increment rotatedihedral crdset <COORDS set> [frame <#>] [name <output set name>] {value <value> | increment <increment>} { <mask1> <mask2> <mask3> <mask4> | res <#> type <dih type> } <dih… Read More
Updated: March 27, 2019
Select the reference for distance-based masks activeref <#> Set which reference structure should be used when setting up distance-based masks for everything but the mask action. Numbering starts from 0, so ’activeref 0’ selects the first reference structure… Read More
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