Tools and information for AMBER and CPPTRAJ examples
Updated: March 27, 2019
Calculate average correlation between motions of specified atoms. atomiccorr [<mask>] out <filename> [cut <cutoff>] [min <min spacing>] [byatom | byres] <mask> Atoms to calculate motion vectors for. out <filename> File to write results to. cut <cutoff> Only print… Read More
Updated: March 27, 2019
Calculate area per molecule for molecules in a specified plane. areapermol [<name>] {[<mask1>] [nlayers <#>] | nmols <#>} [out <filename>] [{xy | xz | yz}] [<name>] Data set name. [<mask1>] Atom mask for selecting molecules. If any atom… Read More
Updated: July 23, 2020
Calculate the angle between three points angle [<dataset name>] <mask1> <mask2> <mask3> [out <filename>] [mass] [<dataset name>] Output data set name. <maskX> Three atom masks selecting atom(s) to calculate angle for. [out <filename>] Output file name. [mass] Use… Read More
Updated: January 26, 2024
Remove specified atoms from the system. strip <mask> [charge <new charge>] [outprefix <prefix>] [nobox] [parmout <filename>] [parmopts <comma-separated-list>] <mask> Remove atoms specified by… Read More
Updated: January 3, 2022
Calculate secondary structure content using the DSSP algorithm secstruct [<name>] [out <filename>] [<mask>] [sumout <filename>][assignout <filename>] [totalout <filename> [ptrajformat] [betadetail] [namen <N name>] [nameh <H name>] [nameca <CA name>][namec <C name>] [nameo <O name>] [<name>] Output data set… Read More
Updated: April 6, 2023
Perform best fit of coordinates to reference and calculate coordinate RMSD. rmsd [<name>] <mask> [<refmask>] [out <filename>] [mass] [nofit | norotate | nomod] [savematrices [matricesout <file>]]… Read More
Updated: November 20, 2024
Perform math on given vector data sets. vectormath vec1 <vecname1> vec2 <vecname2> [out <filename>] [norm] [name <setname>] [ dotproduct | dotangle | crossproduct | magnitude ] vec1 <vecname1> vec2 <vecname2> Vector(s) on which to operate. [out <filename>] Name… Read More
Updated: March 25, 2019
Calculate eigenvectors and eigenvalues from given symmetric matrix. diagmatrix <name> [out <filename>] [thermo [outthermo <filename>]] [vecs <#>] [name <modesname>] [reduce] [nmwiz [nmwizvecs <#>] [nmwizfile <filename>]] <name> Name of symmetric matrix to diagonalize. [out <filename>] Write results to <filename>…. Read More
Posted: February 21, 2019
matrix [out <filename>] [start <#>] [stop|end <#>] [offset <#>] [name <name>] [ byatom | byres [mass] | bymask [mass] ] [ ired [order <#>] ] [ {distcovar | idea} <mask1> ] [ {dist | correl | covar |… Read More
Updated: August 30, 2023
cpptraj [-p <Top0>] [-i <Input0>] [-y <trajin>] [-x <trajout>][-ya <args>] [-xa <args>] [<file>] [-c <reference>] [-d <datain>] [-w <dataout>] [-o <output>] [-h | –help] [-V | –version] [–defines] [-debug <#>] [–interactive] [–log <logfile>] [-tl] [-ms <mask>] [-mr <mask>]… Read More
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