Introductory 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 (based on an original DNA tutorial developed by Thomas Cheatham)
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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 |
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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). Then we set up a simulation of
sustiva bound to HIV-RT. |
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By Ross Walker and Sishi Tang
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Ukrainian translation |
| Another basic
tutorial for setting up a protein-ligand system
has been prepared by Dmitry Nylov. |
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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: Setting up a
DNA-Ligand System |
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This tutorial covers setting up an advanced system. In this
case it shows you how to set up a dye system that is covalently
bound to DNA. It also includes manually running
multiconformational RESP fits, building custom units and
assigning parameters manually. |
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By Bryan Leland, David Paul, Brent Krueger and Ross
Walker
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| TUTORIAL A1 Old: Building your own Custom Residues
(old version) |
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This tutorial is somewhat replaced by tutorial A1 above,
however, it is kept here since it does show a useful example of
how to create a system containing a metal atom. 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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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. |
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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 to calculate the binding energy of the RAS-RAF
protein complex. It also includes instructions on using the
mmpbsa_py script (in Amber11) to perform these calculations as well. |
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By Ross Walker & Thomas Steinbrecher
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| TUTORIAL A4: NMR Refinement
of DNA and RNA Duplexes |
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This tutorial provides a basic introduction to using AMBER
for NMR refinement of a DNA duplex. It makes use of LEaP and Sander.
[Related information: Mike Summers has prepared a
set
of scripts for RNA refinement.
It contains
descriptions, examples, and scripts that were used to generate
initial structures with cyana and refined with Amber.
Nearly all steps (file conversions, etc.) are written into
scripts so that the process can be followed. Some scripts
may need tweaking, depending on your operating
system. The work is described in:
J. Biomol. NMR 47, 205-219 (2010).]
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By Vickie Tsui & Rhonda Torres
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| TUTORIAL A5: Nudged
Elastic Band [AMBER v11 only] |
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This tutorial uses a feature that is only available with
Amber v11. As such you need to have Amber 11 installed to run the
calculations in this tutorial, if you are using Amber 9 or 10
then you should use the
older NEB 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 Christina Bergonzo, Carlos Simmerling & Ross Walker
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| TUTORIAL A6: pKa Calculations using Thermodynamic Integration [AMBER
v9 and later] |
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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
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This tutorial covers how to setup, run and
postprocess replica exchange simulations using multisander and
Amber 10 or later.
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By Dan Roe, Asim Okur, Carlos Simmerling and Ross
Walker
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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
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| 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 or later,
and how to run and analyze a short free energy calculation |
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By Thomas Steinbrecher
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| TUTORIAL A10:
Steered molecular dynamics of a proton transfer reaction |
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This tutorial illustrates the use of
steered molecular dynamics and a QM/MM energy to compute the barrier to proton
trasnfer in malonaldehyde. |
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By M.L. Dodson and V. Babin
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| TUTORIAL A11:
Conformational equilibria of methyl-alpha-L-iduronic
acid in explicit water |
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This tutorial illustrates the use of
conformational "flooding" to setup a Hamiltonian replica exchange simulation
of a small molecule in explicit solvent. |
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By V. Babin and C. Sagui
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| TUTORIAL A12:
Conformational equilibria of poly-proline pentamer
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This tutorial describes a couple of ways
to assess conformational equilibria of a short polyproline peptide using
so called steered molecular dynamics, and the famous replica-exchange
protocol:
html,
pdf,
polyproline-tutorial-files.tar.bz2 (Warning: 60Mb).
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By V. Babin and C. Sagui
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| TUTORIAL A13:
Simulation of a protein crystal
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This tutorial describes one way to set up
a simulation of a protein crystal, showing how to construct unit cells, and
how to fill in missing solvent.
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By Dave Cerutti
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| TUTORIAL A14:
Using 3D-RISM to place waters
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This tutorial shows how the 3D-RISM
method can be used to generate an initial configuration of water around a
solute molecule.
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By Daniel Sindhikara
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| TUTORIAL A15:
Simulations of a room-temperature ionic liquid
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This tutorial illustrates the use of
antechamber and sander to carry out some simple simulations of a
room-temperature (non-biological!) ionic liquid.
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By Chris Lim
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| TUTORIAL A16: Lipid Bilayers with an Amber Lipid Force Field
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Phospholipid bilayers are the stage where many essential biophysical and biochemical processes take place. Between the intracellular and extracellular environments, the lipid bilayer itself is an important component. This tutorial explains how to set up and simulate some simple lipid bilayers with the Lipid11 force field. A DOPC bilayer is built, converted, and loaded into LEaP to assemble the parameters for molecular dynamics simulation. A simple minimization, heating, and production scheme is presented followed by a simple analysis of the trajectory. Furthermore, membrane-bound proteins are examined and a simple membrane-bound protein system is built.
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By Ben Madej & Ross Walker
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TUTORIAL A17:
Umbrella Sampling Example - Calculating the PMF for Alanine
Dipeptide Phi/Psi Rotation |
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In this tutorial we will learn how to use
the AMBER software coupled with the Weighted
Histogram Analysis Method (WHAM) of Alan
Grossfield to generate potentials of mean force.
Often one might want to know what the free
energy profile is along a specific reaction
coordinate. Such a profile is known as a
potential of mean force and it can be very
useful for identifying transition states,
intermediates as well as the relative
stabilities of the end points. At first thought
one might think that you could generate a free
energy along a specific reaction coordinate by
just running an MD simulation and then looking
at the probabilities of the states sampled.
However, often the energy barrier of interest is
many times the size of kbT and so the
MD simulation will either remain in the local
minimum it started in or cross to different
minima but very very rarely sample the
transition state. Umbrella sampling offers a way
to effectively force the system to move through
a transition state and reaction pathway that
chemical knowledge of the system under study
suggests is important. |
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By Ross Walker & Thomas
Steinbrecher
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TUTORIAL A18:
Constant pH Molecular Dynamics Example - Calculating
pKas for titratable side chains in HEWL |
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In this tutorial we will learn how to use
the AMBER software to perform molecular dynamics simulations at constant
pH (CpHMD). Solution pH affects titratable side chains in proteins (and,
on occasion, ribozymes), which can have a dramatic impact on the function,
structure, and stability of large biomolecules. CpHMD is a method that
uses a hybrid molecular dynamics/Monte Carlo approach to sample
conformations and protonation states of various titratable residues in
biomolecules. This method can help capture the coupling between protein
structure and pH.
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By Jason Swails & T. Dwight McGee Jr.
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