(Note: These tutorials are meant to provide illustrative examples of how to use the AMBER software suite to carry out simulations that can be run on a simple workstation in a reasonable period of time. They do not necessarily provide the optimal choice of parameters or methods for the particular application area.)
Copyright Ross Walker 2015

Simulating a DNA polyA-polyT Decamer

Formerly known as TUTORIAL B1

By Ross Walker
based on an original DNA tutorial developed by Thomas Cheatham

Updated for AMBER 15
^{[by
Aditi Munshi and Ross Walker]}

Updated for AMBER 18
_{[by Sifath Mannan, Michael Barton and Tyler Luchko]}

The average structure from a 1 nanosecond molecular dynamics simulation of a 10 base pair poly(A)-polt(T) DNA duplex. The calculation was run in explicit solvent using periodic boundaries and the particle mesh Ewald method of treating long range electrostatics. The average structure was generated using cpptraj by RMS fitting all of the DNA atoms in 1,000 snapshots at 1 ps intervals and then averaging the coordinates.

Section 1: Introduction

The purpose of this tutorial is to provide an initial introduction to setting up and running simulations using the AMBER software (It is based on AMBER 10 and AmberTools 1.2 but should be used with AMBER 14 and AmberTools 15). In this tutorial we run a series of simulations on a poly(A)-poly(T) decamer of DNA. We will first figure out how to generate a starting structure and then use this structure to construct the necessary input files for running sander, the main molecular dynamics engine supplied with AMBER 14.

In order to run a classical molecular dynamics simulation with sander a number of files are required. These are (using their default file names):

prmtop - a file containing a description of the molecular topology and the necessary force field parameters.
rst7 (or a restrt from a previous run) - a file containing a description of the atom coordinates and optionally velocities and current periodic box dimensions.
mdin - the sander input file consisting of a series of namelists and control variables that determine the options and type of simulation to be run.

In the first section of this tutorial we shall use the tools provided with AmberTools 15 to create prmtop and rst7 files for both in-vacuo and solvated systems. We will then run sander to perform minimization followed by molecular dynamics and eventually get to the point where we can reproduce the picture shown above.

Since running these simulations using explicit solvent can be expensive, we will also use some models that include solvent effects implicitly.

The approximate order of this tutorial will be as follows:

Create the prmtop and rst7 files: This is a description of how to generate the initial structure and set up the molecular topology/parameter and coordinate files necessary for performing minimization or dynamics with sander.
An introduction to minimization and molecular dynamics. Run short MD simulations in-vacuo. Perform basic analysis such as calculating root-mean-squared deviations (RMSd) and plotting various energy terms as a function of time. Visualizing results with VMD.
Minimization and molecular dynamics in implicit solvent: Setting up and running equilibration and production minimization and molecular dynamics simulations for our DNA model using the Born implicit solvent model.
Minimization and molecular dynamics in explicit solvent: Setting up and running equilibration and production simulations for our DNA model using TIP3P explicit water.

Throughout this tutorial file names and command line switches will be written in courier or an equivalent monospace font while program names such as sander will be written in the same font but italicized.

Please note that this tutorial assumes that you have AMBER 15 and AmberTools successfully installed and that all the test cases pass. It also assumes that you have VMD installed. For details on VMD please see: http://www.ks.uiuc.edu/Research/vmd/

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