Tools and information for AMBER and CPPTRAJ examples
Updated: August 30, 2021
Cluster Analysis with CPPTRAJ One way of determining structure populations from simulations is cluster analysis. Clustering is a means of partitioning data so that data points inside a cluster are more similar to each other than they are… Read More
Category: CPPTRAJ recipes, General
Updated: July 13, 2023
Principal component analysis with CPPTRAJ The goal here is to perform principal component analysis (PCA) using CPPTRAJ on two different trajectories of a 36-mer double stranded DNA, d(GCACGAACGAACGAACGC). One of the trajectories was run on GPUs and the… Read More
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: August 30, 2021
You want to see if a region of a protein is presenting high fluctuations and conformation changes. Sometimes is useful to detect regions of a system that have elevated motions and fluctuations. The fastest way to see this… Read More
Category: CPPTRAJ recipes, General
Updated: June 14, 2023
You need to extract a representative structure from three independent runs of a protein simulation. In this example, we will use the 575 amino acid tyrosine phosphatase from the PDB code 1LAR. We have included an inhibitor in… Read More
Category: CPPTRAJ recipes, General
Updated: May 27, 2019
You want to filter certain frames from a trajectory for further post-processing. In a ligand-receptor system, the ligand could be exploring different regions of the receptor over time. In order to select frames that contain a specific ligand… Read More
Category: CPPTRAJ recipes, General
Updated: May 20, 2019
You want to compare the structural difference caused by the binding of 6 different ligands to the same protein receptor. First we need to create a reference structure that has no ligand that will serve to compare the… Read More
Updated: July 23, 2021
You want to calculate how much time is spent in a particular conformation or state from a simulation between a small molecule and a receptor. The calcstate command can follow multiple geometric datasets (like those generated by the… Read More
Category: CPPTRAJ recipes, General
Updated: November 29, 2022
You want to obtain the value of multiple dihedral angles from a protein. It is very common to study the stability of a system through the distributions of specific angles, to see if there is any type of … Read More
Category: CPPTRAJ recipes
Updated: August 7, 2021
Sometimes is useful to present the data as a distribution of values. CPPTRAJ can calculate a histogram for a particular dataset using the hist command. Using an example data of a double stranded 18-mer DNA with sequence… Read More
Category: CPPTRAJ recipes
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