Tools and information for AMBER and CPPTRAJ examples
Updated: April 5, 2022
This example consists of a full set of instructions that will guide the user on how to run a simulation using AMBER and performing the analysis with CPPTRAJ. In this tutorial, we will run a DNA molecule with… Read More
Updated: March 26, 2019
Project coordinates along given eigenvectors. projection [<name>] evecs <dataset name> [out <outfile>] [beg <beg>] [end <end>] [<mask>] [dihedrals <dataset arg>] [start <start>] [stop <stop>] [offset <offset>] [<name>] Output data set name. evecs <dataset name> Data set containing eigenvectors… Read More
Updated: March 27, 2019
Retain only the specified number of solvent molecules closest to specified solute. closest <# to keep> <mask> [noimage] [first | oxygen] [center][closestout <filename>] [name <setname>] [outprefix <parmprefix>][parmout <file>] <# to keep> Number of solvent molecules to keep around… 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: 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
Updated: March 25, 2019
Calculate auto or cross correlation for 1 or 2 data sets. corr out <outfilename> <dataset1> [<dataset2>] [lagmax <lag>] [nocovar] [direct] out <outfilename> Write results to file named <outfilename>. The datasets must have the same # of data points…. Read More
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