multipucker
Calculate specified pucker types for residues in given range. multipucker [<name>] [<pucker types>] [out <filename>] [resrange <range>] … Read More
Updated: January 12, 2024
Calculate specified pucker types for residues in given range. multipucker [<name>] [<pucker types>] [out <filename>] [resrange <range>] … Read More
Category: Action Commands, CPPTRAJ
Updated: November 11, 2023
Calculate extended comparison similarity values for each frame in COORDS set. extendedcomp <input crd set> [name <output data set>] [metric <metric>] [out <file>]… Read More
Category: Coordinates Data Set commands, CPPTRAJ
Updated: November 11, 2023
Apply Z-matrix to a COORDS set or calculate Z-matrix for a molecule/frame in a COORDS set. zmatrix <COORDS set name> [name <output set name>] { zset <input zmatrix set> [parm <top>|parmindex <#>] | … Read More
Category: Coordinates Data Set commands, CPPTRAJ
Updated: November 18, 2023
Create a new molecule from a sequence of COORDS sets. sequence name <output set name> <unit0> <unit1> … [{libset <libsetname>} …] name <output set name> Name of final molecule. <unit0> <unit1> Name of COORDS set (with connection info)…. Read More
Category: Coordinates Data Set commands, CPPTRAJ
Posted: November 11, 2023
Transform a COORDS set in one of several ways. crdtransform <input crd set> [name <output crd set>] { rmsrefine [mask <mask>] [mass] [rmstol <tolerance>] | normcoords | trim [metric <metric>] [{ntrimmed <#>|cutoff… Read More
Category: Coordinates Data Set commands, CPPTRAJ
Updated: September 9, 2023
Parse timing data from CPPTRAJ output. parsetiming … [out ] [name ] [sortby {time|cores|filename}] [includebad] [showdetails] [type {trajproc|trajread|actframe}] [reverse] [groupout [grouptype {prefix|name|kind}]] <filename args> Files containing CPPTRAJ output to get timing data from. [out <file>] Write total sorted… Read More
Category: General Commands
Updated: July 13, 2023
Update/add parameters in/to a topology. parm <name> | parmindex <#> setname <parm set> parm <name> | parmindex <#> Topology to update. setname <parm set> Topology or parameter data set containing parameters to use. NOTE: This command is provided… Read More
Category: CPPTRAJ, Topology File Commands
Posted: July 1, 2023
Print Urey-Bradley info for selected atoms. printub [parm <name> | parmindex <#> | <#>] [<mask1>] [<mask2>] [out <file>] [parm <name> | parmindex <#> | <#>] Name/tag or index of topology. Default is first loaded topology. [<mask1>] Atoms to… Read More
Category: CPPTRAJ, Topology File Commands
Posted: July 1, 2023
Read cpin <file> cpin <file> Constant pH input (CPIN) file name. Note that when reading in constant pH data the data set aspect will be set to the residue name and the index will be set to the… Read More
Category: CPPTRAJ, Data File Options
Posted: May 30, 2023
Calculate average unit cell (box), primarily for unwrapping NPT trajectories. avgbox [name ] [out ] [name ] Average unit cell data set name. [out <file>] File to write average unit cell data to. DataSets created:… Read More
Category: Action Commands, CPPTRAJ
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