Category: Data Sets and Data Files

prepareforleap

Updated: February 28, 2024

Prepare a structure (usually loaded from a PDB) for processing with LEaP from Amber. prepareforleap crdset <coords set> [frame <#>] name <out coords set> [pdbout <pdbfile> [terbymol]] [leapunitname <unit>] [out <leap input file> [runleap… Read More

Category: CPPTRAJ, Data Sets and Data Files

splitcoords

Posted: April 5, 2022

Split molecules in a COORDS set into a trajectory. splitcoords <crd set> name <output set name> <crd set> COORDS set to split. name <output set name> Name of new set to create. Split trajectory specified by <crd set>… Read More

Category: CPPTRAJ, Data Sets and Data Files

Data Set Selection Syntax

Updated: November 18, 2023

Many analysis commands can be used to analyze multiple data sets. The general format for selecting data sets is: <name>[<aspect>]:<index> The ’*’ character can be used as a wild-card for entire names (no partial matches). <name>: The data… Read More

Category: CPPTRAJ, Data Sets and Data Files

Tags: data fi, data files, data sets

Data Set Math

Updated: November 18, 2023

Operations with data sets As of version 15, CPPTRAJ can perform basic math operations, even on data sets (with some limitations). Currently recognized operations are: Operation Symbol Minus – Plus + Divide / Multiply * Power ^ Negate… Read More

Category: CPPTRAJ, Data Sets and Data Files

Tags: data files, data sets