Tools and information for AMBER and CPPTRAJ examples
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: March 27, 2019
Run a single Action on a COORDS set
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: March 25, 2019
Calculate autocorrelation function for multiple data sets. autocorr [name <dsetname>] <dsetarg0> [<dsetarg1> …] [out <filename>] [lagmax <lag>] [nocovar] [direct] <dsetarg0> [dsetarg1> …] Argument(s) specifying datasets to be used. [name <dsetname>] Store results in dataset(s) named <dsetname>:X. [out <filename>]… Read More
Updated: January 12, 2024
Calculate average, standard deviation, min, and max for (or over) data sets. Not to be confused with the average command. avg <dset0> [<dset1> …] [torsion] [out <file>] [oversets] [name <name>] [nostdout] <dsetX> Data set(s) to calculate the average… Read More
Updated: March 30, 2019
Calculate states based on given data sets and criteria. calcstate {state <ID>,<dataset>,<min>,<max>} [out <state v time file>] [name <setname>] [curveout <curve file>] [stateout <states file>] [transout <transitions file>] state <ID>,<dataset>,<min>,<max> Define a state according to given data set… Read More
Updated: July 1, 2023
Cluster input frames using the specified clustering algorithm and distance metric. cluster [crdset <crd set>] [data <dset0> [,<dset1>…]] [nocoords] [<name>] [<Algorithm>] [<Metric>] [<Pairwise>] … Read More
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