[Pictured below is an average structure taken over 1 nanosecond from a solvated particle mesh Ewald simulation of a decamer poly(A)-poly(T) duplex. The average structure was created using carnal to RMS fit and coordinate average all DNA atoms from the trajectory taken at 1 picosecond intervals.] (picture of B-DNA)

DNA:DNA, polyA-polyT

The purpose of this tutorial is to demonstrate how to set up a standard decamer poly(A)-poly(T) duplex DNA model structure using the tools provided with AMBER. This tutorial is based on version 7.0 of AMBER.

In this discussion, we first figure out how to generate a starting structure and then use this structure to build up the input files necessary for running sander, the main molecular dynamics engine supplied with the AMBER suite of programs. The basic files necessary to run sander (named as the default names) are:

prmtop: a description of the molecular topology and force field parameters
inpcrd (or a restrt from a previous run): a description of the coordinates and optionally the velocities and current box dimensions
mdin: the sander input file which is a series of namelists and control variables

After we've built up the prmtop and inpcrd files, for in vacuo and solvated systems, we will actually run sander to perform minimization and molecular dynamics and eventually get to the point where we can create the picture shown above.

Since running these calculations in solvent is rather expensive, we will also use some models with an implicit solvent (i.e. gas phase calculation with solvent effects added implicitly) which are more tractable and can be run in a few minutes to give a picture of the dynamics...

For the simulations in explicit solvent, this tutorial will include a description of one possible way to "equilibrate" the system and then move into a brief discussion of performing "production" molecular dynamics runs.

All of the simulations in explicit solvent will be run using the particle mesh Ewald (PME) method [ J. Chem. Phys. 103, 8577-8593. (1995) ] within AMBER. Although information is provided on how to run these yourself, at this point we advise that you simply read through this section to get some familiarity, and then proceed on to the next section (analysis) using trajectories we have supplied.

The flow of this tutorial is as follows:

Create the prmtop and inpcrd 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 AMBER.
Getting a feel for minimization and molecular dynamics: Run short MD simulations in-vacuo and with various implicit solvent models. Perform basic analysis such as calculating root-mean-squared deviations (RMSd) and plotting various energy terms as a function of time.
Equilibration and production: Setting up and running equilibration and production minimization and molecular dynamics simulations for our DNA model, in explicit solvent.
Analyzing the results!

thomas <cheatham@chpc.utah.edu>>