Basic Tutorials |
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TUTORIAL B1: Simulating a small fragment of DNA
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This tutorial will act as a basic introduction to LEaP,
sander and ptraj, to build, solvate, run molecular dynamics and analyse
trajectories. It will also cover visualising trajectories using
VMD. The
aim of this tutorial is to act as a brief introduction to running classical
molecular dynamics simulations using the AMBER software. In this tutorial
we will create a initial structure for a 10-mer of DNA and
then we will run gas phase, implicit and explicit solvent
simulations on it. Finally we will look at a practical
example of how MD simulations can be used to investigate how
A-DNA can convert to B-DNA. |
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By Ross Walker
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| TUTORIAL B2: Using VMD
with AMBER |
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This tutorial acts as a brief introduction to using
VMD for
visualising AMBER inpcrd, restrt and trajectory files. While only scratching
the surface of what VMD can do it covers setting up a .vmdrc file to set the
default layout of VMD, loading static structures and performing RMSD fits
between similar structures. It then goes on to cover loading and visualising
AMBER trajectories, both from gas phase/implicit solvent simulations and
from periodic boundary simulations and shows how to save individual frames
from a trajectory as well as create an MPEG video of the trajectory. |
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By Ross Walker
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TUTORIAL B3: Case
Study - Folding TRP Cage (Advanced analysis and clustering)
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This tutorial is designed as a
case study that will show you how to reproduce the work discussed in the
following paper:
Simmerling, C., Strockbine, B., Roitberg, A.E., J. Am. Chem. Soc., 2002,
124, 11258-11259
(http://dx.doi.org/10.1021/ja0273851)
It is a fairly long and in-depth tutorial covering creating structures using
XLeap followed by running heating and long MD simulations to conduct protein
folding experiments. It then moves on to more advanced analysis, including
RMSd fitting, mdcrd to binpos conversion, average structure
calculation, hydrogen bond analysis and dihedral angle tracking using ptraj.
We also look at cluster analysis using the MMTSB toolset. It is recommended that
you complete the earlier tutorials in this listing before attempting this
more advanced tutorial. This tutorial has been updated to cover both AMBER 8
and AMBER 9. |
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By Ross Walker
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| TUTORIAL B4: Simulating a pharmaceutical compound using
antechamber and the Generalized Amber Force Field. |
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Antechamber is a set of tools, shipped with AMBER, that can
be used to prepare "prep" input files for organic molecules, which can then
be read into LEaP and used to create prmtop and inpcrd files. The
Antechamber suite is designed for use with the "general AMBER force field
(GAFF)" and is ideal for setting up simulations involving organic
pharmaceutical compounds or other organic molecules. In this tutorial we
will use antechamber to create a leap input file for BMS's HIV reverse
transcriptase inhibitor sustiva (efavirenz). |
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By Ross Walker
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| TUTORIAL B5: Demo of Ptraj Commands |
This tutorial illustrates how to use AMBER's ptraj analysis
program to analyse a peptide simulation and gather a range of statistics
from the trajectory.
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By Jim Caldwell
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| TUTORIAL B6: Visualizing Amber Trajectories with Sirius |
This tutorial illustrates how to use San Diego Supercomputer Center's
Sirius visualization software to display and analyze AMBER MD trajectory and output files. This
includes realtime secondary structure updates, realtime energy, temperature plots as well as flexible
calculation of RMSD along the trajectory. It also highlights how to produce high quality still images (ray traced)
and videos of AMBER trajectories. It also explains how to load compressed trajectory and output files on the fly,
make use of buffered loading to display very large trajectory files and make edits to structures.
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By Sasha Buzkho
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Advanced Tutorials |
| TUTORIAL A1: Building your own Custom Residues |
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Often you will want to simulate a protein system that
contains a non-standard residue such as a co-enzyme or an
inhibitor. In this case you cannot simply build the topology and
coordinate files. You first need to generate a new unit in xleap,
add any missing parameters and charges and then create your
prmtop and inpcrd files. If the non-standard residue is a
standalone molecule then you could use Antechamber for this (see
tutorial B4). However, in this this tutorial we will model plastocyanin which has a copper atom bound to four close
residues. This tutorial will give an example of how to build
this residue unit in xleap.
There are two versions of this tutorial. A
simple version which creates just a new copper residue and
approximates it as a +1 ion and a more
advanced version where new special histidine and methionine
residues are created so that different charges and bond / angle
and dihedral parameters can be used. |
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By Ross Walker
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| TUTORIAL A2: A simple
coupled potential QM/MM/MD simulation. |
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(Updated for AMBER 9): The tutorials up to this point
have all used the classical amber force field equation to minimise the
system and propagate the dynamics. With the release of AMBER 9 comes the
ability to do very fast advanced coupled potential QM/MM driven minimisation
and MD. This tutorial will show how to set up a simple QM/MM/MD simulation
of NMA in solution using AMBER 9. Although AMBER 8 is no longer recommended
for running QM/MM MD simulations An AMBER 8 version of this tutorial is
available here. |
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By Ross Walker
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| TUTORIAL A3: MM-PBSA |
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This tutorial provides a step by step explanation of using
the mm_pbsa script in AMBER 9 to calculate the binding energy of the RAS-RAF
protein complex.
(There is also an alternative MM-PBSA tutorial prepared by
Bethany Kormos and Dave Beveridge. These are in pdf format and available in two
versions. One for AMBER
version 7 and one for AMBER
versions 8 & 9.) |
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By Ross Walker & Thomas Steinbrecher
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| TUTORIAL A4: NMR Refinement of a DNA Duplex |
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This tutorial provides a basic introduction to using AMBER
for NMR refinement. It makes use of LEaP and Sander. |
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By Vickie Tsui & Rhonda Torres
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| TUTORIAL A5: Nudged Elastic Band [AMBER v9 only] |
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This tutorial uses a feature that is only available with
Amber v9. As such you need to have Amber 9 installed to run the
calculations in this tutorial. In the nudged elastic band
method,
the path for a conformational change is approximated with a
series of images of the molecule describing the path.
Minimisation of the entire system, but with the end point
structures fixed, provides a minimum energy path. In this
tutorial we will use the NEB method to predict a pathway for a
conformational change in alanine dipeptide. |
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By Ross Walker
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| TUTORIAL A6: pKa Calculations using Thermodynamic Integration [AMBER
v9 only] |
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This tutorial reproduces the calculation of the
pKa value of the ASP residue in the protein thioredoxin as
described in the following paper:
Simonson, T., Carlsson, J., Case, D.A.,
"Proton Binding to Proteins: pKa Calculations with Explicit
and Implicit Solvent Models", JACS 2004, 126, pp4167-4180.
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By Ross Walker & Mike Crowley
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| TUTORIAL A7: Replica Exchange [Coming Soon] |
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| TUTORIAL A8: Loop dynamics of the HIV-1 integrase core domain |
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This tutorial is a walk-through of one of Prof Matt Lee's
research projects. It will take you through how to setup, run
and analyze a simulation of the core domain of the HIV-1 integrase enzyme. |
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By Matt Lee |
| TUTORIAL A9: Thermodynamic Integration using soft core potentials |
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This tutorial computes the relative binding free energy of two ligands bound to a lysozyme mutant.
In three steps, you will learn about the background of soft core TI calculation, the new system setup for Amber10
and how to run and analyze a short free energy calculation |
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By Thomas Steinbrecher |
