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BEGINNING AMBER WORKSHOP

This online workshop provides an introduction to the AMBER molecular dynamics software and

molecular dynamics and visualisation in general. The workshop consists of a series of tutorials

from beginner level to advanced. These tutorials are designed to cover running simple

minimisations and MD simulations using the sander module of the amber software as well as how

to set-up calculations and what to do with non-standard residues. Ideally you should work through

these tutorials in the order they appear.

Where to get Help and Information

The first question people ask when confronted with a new piece of software is where can I get help? Amber is no

different. Amber is a very sophisticated piece of scientific software and as such can appear very daunting to the

new user. Fortunately there are a number of places both new and experienced users can go to get help. The best

source of help for active users of the Amber software is the amber mailing list

and the mailing list archive.

Questions sent to this list will go to all active amber uses and so you get the help of the amber community.

Mailing list archive: http://amber.ch.ic.ac.uk/archive

(all messages posted on the mailing list are stored here).

Mailing list signup information: http://amber.scripps.edu/#reflector

For new uses there are, in addition to these tutorials a number of tutorials (of varying quality) available on the

amber website: http://amber.scripps.edu/tutorial/index.html

Other sources of information include the Amber manual (Version 9: http://amber.scripps.edu/doc9/amber9.pdf

Version 8: http://amber.scripps.edu/doc8/amber8.pdf

) as well as the amber website (http://amber.scripps.edu).

Also remember this: GOOGLE is your friend.

You can search the web, the mailing list archive or these tutorials using the following box:

Some Background

"Amber" refers to two things: a set of molecular mechanical force fields for the simulation of

biomolecules (which are in the public domain, and are used in a variety of simulation programs);

and a package of molecular simulation programs which includes source code and demos. The

current version of the code is Amber version 9, which is distributed by TSRI & UCSF subject to a

licensing agreement described on the amber website.

A good general overview of the Amber codes can be found in: D.A. Pearlman, D.A. Case, J.W.

Caldwell, W.R. Ross, T.E. Cheatham, III, S. DeBolt, D. Ferguson, G. Seibel and P. Kollman.

AMBER, a computer program for applying molecular mechanics, normal mode analysis,

molecular dynamics and free energy calculations to elucidate the structures and energies of

molecules. Comp. Phys. Commun. 91, 1-41 (1995).

An overview of the Amber protein force fields, and how they were developed, can be found in:

J.W. Ponder and D.A. Case. Force fields for protein simulations. Adv. Prot. Chem. 66, 27-85

(2003). Similar information for nucleic acids is given by T.E. Cheatham, III and M.A. Young.

Molecular dynamics simulation of nucleic acids: Successes, limitations and promise. Biopolymers

56, 232-256 (2001).

In this workshop the word amber will refer to the software package which we will be using to run

simulations controlled via the Amber force field.

The release consists of about 50 programs, that work reasonably well together. The major

programs are as follows:

• sander: Simulated annealing with

NMR-derived energy restraints. This

allows for NMR refinement based on

NOE-derived distance restraints, torsion

angle restraints, and penalty functions

based on chemical shifts and NOESY

volumes. Sander is also the "main"

program used for molecular dynamics

simulations, and is also used for

replica-exchange, thermodynamic

integration, and potential of mean force

(PMF) calculations. AMBER 9 also

includes all new QM/MM support.

• pmemd: This is an extensively-modified

version (prepared by Bob Duke) of the

sander program, limited to periodic, PME

simulations. It is faster, and scales better

on parallel machines, than sander; hence

it is usually the program of choice for

"standard", periodic simulations that do

not require features it does not support.

The AMBER 9 version of pmemd also

has support for implicit solvent

Generalized Born simulations.

• nmode: Normal mode analysis program

using first and second derivative

information, used to find search for local

minima, perform vibrational analysis, and

search for transition states.

• LEaP: LEaP is an X-windows-based

program that provides for basic model

building and Amber coordinate and

parameter/topology input file creation. It

includes a molecular editor which allows for

building residues and manipulating

molecules.

• antechamber: This program suite

automates the process of developing force

field descriptors for most organic

molecules. It starts with structures (usually

in PDB format), and generates files that can

be read into LEaP for use in molecular

modeling. The force field description that is

generated is designed to be compatible

with the usual Amber force fields for

proteins and nucleic acids.

• ptraj: This is used to analyze MD

trajectories, computing a variety of things,

like RMS deviation from a reference

structure, hydrogen bonding analysis,

time-correlation functions, diffusional

behavior, and so on.

• mm_pbsa: This is a script to automate

post-processing of MD trajectories, to

analyze energetics using continuum solvent

ideas. It can be used to break energies

energies into "pieces" arising from different

residues, and to estimate free energy

differences between conformational basins.

In this workshop due to time restraints we will largely concentrate on using the sander module of

Amber to run molecular dynamics simulations. For this we will use the following programs from

the amber suite: sander, xleap, ptraj and antechamber. For introductions to the other programs

available please see the Amber 9 manual and the online tutorials. Note these tutorials were largely

designed for Amber 8, they are currently being updated for Amber 9. Most of the tutorials should

be equally applicable to either Amber v8 or Amber v9.

Workshop Tutorials

(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.)

TUTORIAL 1: Simulating a small fragment of DNA. (Beginner)

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

. This tutorial is an adaptation of the main DNA tutorial provided with the

AMBER software. It's aim is to act as a brief introduction to running classical molecular

dynamics simulations using the AMBER software. If you are already familiar with AMBER

and/or have already completed the online DNA tutorial then you can skip this and move

straight on to tutorial 2.

TUTORIAL 2

: Using dynamics simulations to estimate binding energetics. (Beginner)

The purpose of this tutorial is to begin thinking about how one might estimate energetics

of binding. Here we will obtain some estimated binding energies for a protein ligand

system using a short MD simulation. In this tutorial you will be expected to setup the

calculation yourself using your experience from tutorial 1 and as such the notes will be

much briefer.

TUTORIAL 3

: Examining the pKa's of Asp and Glu residues. (Beginner)

The aim of this tutorial is to show how one can use Amber's GB model and minimisation

routines to estimate the pKa shifts for glutamic acid and aspartic acid residues in proteins.

We will examine two different structures from an NMR ensemble and calculate the pKa

shift in each case. The results should show that the shift in pKa is very much dependent

on the protein conformation.

TUTORIAL 4

: Simulating a solvated protein that contains a non-standard residue.

(Intermediate)

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

5). 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.

TUTORIAL 5

: Simulating a pharmaceutical compound using antechamber and the

Generalized Amber Force Field. (Intermediate)

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).

TUTORIAL 6

: A simple coupled potential QM/MM/MD simulation. (Intermediate)

(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

TUTORIAL 7

: Nudged Elastic Band [AMBER v9 only] (Advanced)

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

1,2

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.

TUTORIAL 8

: Case Study - Folding TRP Cage (Advanced)

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 advanced results analysis including advanced RMSd fitting, mdcrd to binpos

conversion, average structure calculation, hydrogen bond analysis and dihedral angle

tracking using ptraj. As well as 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.

TUTORIAL 9

: Using VMD with AMBER (Intermediate)

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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psfan

2014-01-27

写得很详细，值得参考

xianyuanshan

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