CPPTRAJ cookbook

Recipes and examples to perform analysis using CPPTRAJ.

In addition to the series of recipes, we present a list of fast one-liner CPPTRAJ codes that can be useful in the day to day work for the computational chemist.

All the recipes presented for CPPTRAJ can be run by saving the commands in a text file (i. e. with the name: in.cpptraj) and then executing in the comand line:

cpptraj -i in.cpptraj
Recipes index.
Combining multiple trajectory files into a single trajectory and remove water molecules to save space
Creating a hydrogen-mass repartitioned topology
Reading the OUT files and plotting different properties
Create an ensemble of PDBs from a trajectory
Generating histograms with CPPTRAJ
Histogram analysis of dihedral angle distributions
Hydrogen bond analysis within a protein
Hydrogen bond analysis between a protein and a small molecule
Comparing the structural difference between a series of ligand-protein complex
Detect regions of high mobility in a protein simulation.
Filtering frames based on a distance and creating a new filtered trajectory
Calculate states between a small molecule and a receptor
Clustering a protein simulation from multiple independent copies
Making a 3D histogram of the position of a small molecule around a receptor
Reorienting small molecules to fit the orientation of another molecule
Detect amino acid interactions between a protein receptor and a small peptide
Mapping Ion Density onto Multidomain Complexes
Calculating the radial distribution function of ions around a biomolecule
Compare the surface area of two cyclic peptides
Measure the stacking percentage of a protein-ligand complex
Create a new AMBER-compatible nucleotide to perform MD simulations