Tools and information for AMBER and CPPTRAJ examples
Posted: November 20, 2024
Calculate the minimum or maximum distance between pairs of atoms/residues/molecules {min|max}dist mask1 <mask1> [mask2 <mask2>] [{byatom|byres|bymol}] [noimage] [name <setname>] [out <file>] [resoffset <#>] mask1 <mask1> First mask for selecting atoms. [mask2 <mask2>] Optional second mask for selecting atoms…. Read More
Category: Action Commands, CPPTRAJ
Updated: November 20, 2024
Project data along eigenmodes projectdata evecs <evecs dataset> [name <name>] [out <outfile>] [beg <beg>] [end <end>]{[dihedrals <dataset arg>] | [data <dataset arg> …]} evecs <dataset name> Data set containing eigenvectors (modes). [name <name>] Output data set name. [out… Read More
Category: Analysis Commands, CPPTRAJ
Updated: November 20, 2024
Perform time-independent correlation analysis (TICA) tica { crdset <COORDS set name> [mask <mask>] | data <input set arg1> … } [lag <time lag>] [map {kinetic | commute | none}] [name… Read More
Category: Analysis Commands, CPPTRAJ
Posted: November 20, 2024
Print the bond parameter table. bondparminfo [parm <name>| crdset <set> | parmindex <#> | <#>] [out <file>] [parm <name> | parmindex <#> | <#>] Name/tag or index of topology. Default is first loaded topology. [out <file>] File to… Read More
Category: CPPTRAJ, Topology File Commands
Updated: April 22, 2025
enedecomp Perform per-atom energy decomposition. enedecomp [<name>] [<mask>] [out <filename>] [savecomponents] [pme [cut <cutoff>] [dsumtol <dtol>] [ewcoeff <coeff>]… Read More
Category: Action Commands, CPPTRAJ
Posted: July 12, 2024
addatom – aname <name> [elt <element>] [rname <res name>] [xyz <X> <Y> <Z>] [mass <mass>] [charge <charge>] [outprefix <prefix>] [nobox] [parmout <filename>] [parmopts <comma-separated-list>] This is mostly useful for adding a placeholder “dummy” atom for subsequent actions to… Read More
Category: Action Commands, CPPTRAJ
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
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