Tools and information for AMBER and CPPTRAJ examples
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
Updated: March 31, 2021
You want to process the information included in the AMBER output files and extract the data to make plots vs time. We can use the readdata command in CPPTRAJ to read the output files and store the values… Read More
Category: CPPTRAJ recipes
Updated: October 1, 2023
When simulations start to get long, the raw trajectory files can start to get very large. It is also sometimes more convenient (and faster) to perform analysis in a stripped trajectory (i. e. without explicit water molecules)…. Read More
Category: CPPTRAJ recipes
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