Category: Tutorials

Simulation of a 10-mer DNA with a deoxy-5-methylcytosine residue

Updated: September 9, 2023

Incorporating a modified base (deoxy-5-methylcytosine) into DNA for MD simulation in AMBER. For this example, we are going to incorportate a modified nucleotide (5-Methylcytosine) into the DNA duplex with the sequence d(CGCGCGCGCG)2 at posiiton 3. The result will… Read More

Category: General, Tutorials

Reorienting small molecules

Updated: December 8, 2022

Reorienting small molecules to fit the orientation of another molecule You want to screen a collection of small molecules into a receptor but need to re-orient them to match a starting structure. In this recipe we will use… Read More

Category: CPPTRAJ, CPPTRAJ recipes, General, General Concepts, Topology File Commands, Tutorials

Hydrogen bond analysis within a protein

Updated: April 12, 2023

You want to study the hydrogen-bonds within a protein system This recipe focuses on the analysis of intra-molecular hydrogen bonds as a protein unfolds at high temperature. For an example about hydrogen bonds between two independent systems (i…. Read More

Category: General, Tutorials

Introduction to Principal Component Analysis

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

Category: General, Tutorials

Making a movie from an AMBER trajectory using VMD

Updated: January 15, 2020

You want to generate a nice movie from your trajectory data. Movies are always useful to show a simulation. In this tutorial we are going to use the Visual Molecular Dynamics ‘VMD’ visualizer from developed at the University… Read More

Category: Tutorials, Visualization