AMBER 8 Tutorial - DNA (poly-A-poly-T)

By: Ross Walker
Dept. Molecular Biology,
The Scripps Research Institute,
La Jolla, Ca, 92037, USA
(Based on the original DNA tutorial by Thomas Cheatham)

CONTENTS

1) Introduction (pdf)

2) Setting up duplex DNA: polyA-polyT (pdf)

2.1) Generating the coordinates of the model structure

          2.1.1) Creating our DNA duplex using nucgen
          2.1.2) Loading the structure into Leap
          2.1.3) Alternative ways to view the structures

2.2) What level of simulation am I going to attempt?

2.2.1) The types of simulations to be run in this tutorial

2.3) Building the prmtop and inpcrd files

2.3.1) LEaP

3) Running Minimisation and Molecular Dynamics (in vacuo) (pdf)

3.1) Relax the system prior to MD

          3.1.1) Building the mdin input file
          3.1.2) Running sander for the first time
          3.1.3) Creating PDB files from the AMBER coordinate files

3.2) Running MD in-vacuo

3.3) Analysing the results

          3.3.1) Extracting the energies, etc. from the mdout file
          3.3.2) Calculating the RMSd vs. time
          3.3.3) Visualising the Trajectories with VMD

4) Running Minimisation and Molecular Dynamics (in implicit solvent) (pdf)

4.1) Relax the system prior to MD
4.2) Running MD with generalise Born solvation

5) Running Minimisation and Molecular Dynamics (in explicit solvent) (pdf)

5.1) Equilibrating and running MD solvated poly(A)-poly(T)

          5.1.1) A brief introduction to periodic boundaries
          5.1.2) Choosing a suitable cut off
          5.1.3) Minimisation Stage 1 - Holding the solute fixed
          5.1.4) Minimisation Stage 2 - Minimising the entire system
          5.1.5) Molecular Dynamics (heating) with restraints on the solute
          5.1.6) Running MD Equilibration on the whole system

5.2) Analysing the results to test the equilibration

          5.2.1) Analysing the output files
          5.2.2) Analysing the trajectory files
          5.2.3) Viewing the trajectory
          5.2.4) Re-imaging the trajectory back into the primary box

5.3) Summary

6) A Practical Example (A-DNA) (pdf)

     6.1) Creating the starting structure
     6.2) Creating the sander input files
     6.3) Minimising the system
     6.4) Running initial equilibration
     6.5) Running further equilibration and production MD
     6.6) Analysing the results

File Summary (Links to all files referenced)