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Amber: How to set-up calculations. Preliminary Remarks. Amber is a very sophisticated piece of scientific software and as such requires some amount of time to learn it.

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preliminary remarks
Preliminary Remarks
  • Amber is a very sophisticated piece of scientific software and as such requires some amount of time to learn it.
  • Although Amber may appear very complex at first, it is reasonably straightforward once you understand the basic architecture and option choices.
  • The best source of help for active users of the Amber software is the amber mailing list and the mailing list archive (http://amber.scripps.edu). Questions sent to this list will go to all active amber uses and so you get the help of the amber community.
preliminary remarks1
Preliminary Remarks
  • Have a look at the Amber Home Page: http://amber.scripps.edu
preliminary remarks importance of visualization
Preliminary Remarks:Importance of Visualization
  • One quick look at the structure can help to detect errors and save days or weeks of your time
importance of visualization real life example
Importance of Visualization: Real Life Example

A person spent many days trying to minimize a structure using Gaussian…

It was no success…

One quick look immediately discovered a problem

Problem

importance of visualization real life example1
Importance of Visualization: Real Life Example

A person spent many days running Molecular Dynamics using Amber…

He was experiencing crashes of Amber during his runs …

Visual inspection of his molecular structures showed that initial structures had had not well prepared.

Oxygen atom is missing

Incomplete valencies on atoms…

Hydrogen atom is missing

The structure also had a steric clash between two amino acid residues which could lead to a program overflow error

freeware visualization programs rasmol
Freeware Visualization Programs:RasMol

http://www.openrasmol.org/

freeware visualization programs vmd
Freeware Visualization Programs:VMD

http://www.ks.uiuc.edu/Research/vmd/

freeware visualization programs gopenmol
Freeware Visualization Programs:gOpenMol

http://www.csc.fi/gopenmol/

freeware visualization programs chimera
Freeware Visualization Programs:Chimera

http://www.cgl.ucsf.edu/chimera/

freeware visualization programs jmoleditor
Freeware Visualization Programs:JMolEditor

It is a Java program, i.e. it is cross-platform

We plan to add support for all Amber and Gaussian input and output files

http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.html

if you are really serious about biomolecular simulations
If you are really serious about Biomolecular Simulations…
  • … you will need an expert molecular modeling environment which provides construction, editing, and visualization tools for both large and small molecules
  • Tripos (www.tripos.com)
  • Accelrys (http://www.accelrys.com)
  • and others…
amber basic tutorials
Amber Basic Tutorials
  • Amber distribution CD comes with several basic tutorials(under amber9/tutorial):

Additional tutorial examples are available at http://amber.scripps.edu.

basic steps for running simulation
Basic Steps for Running Simulation
  • Obtain starting Coordinates (PDB, NMR, Database, Program generated)
  • Run LEaP to generate the parameter and topology file.
  • Run Simulation (sander or pmemd)
  • Analyse the results (ptraj)
information flow in amber
Information Flow in Amber

PDB

antechamber

LEap

Preparatory Programs

Analysis Programs

Topology and

coordinate files

mm-pbsa

ptraj

sander, pmemd,

nmode

Simulation

Programs

Simulation Results

introduction to leap
Introduction to LEaP
  • The name LEaP is an acronym constructed from the names of the older AMBER software modules it replaces: link, edit, and parm.
  • Thus, LEaP can be used to prepare input for the AMBER molecular mechanics programs.
  • LEaP is the generic name given to the programs teLeap and xaLeap, which are generally run via the tleap and xleap shell scripts.
  • These two programs share a common command language
  • The xleap program has been enhanced through the addition of an X-windows graphical user interface.
using tleap the user can
Using tleap, the user can:
  • Read and write files in many formats (PDB, Mol2, Amber Prep, Amber Parm, Object File Format)
  • Construct new residues and molecules using simple commands
  • Link together residues and create nonbonded complexes of molecules
  • Place counterions around a molecule
  • Solvate molecules in arbitrary solvents
  • Modify internal coordinates within a molecule
  • Generate files that contain topology and parameters for AMBER.
with xleap the user can
With Xleap the user can:
  • Access commands using a simple point and click interface
  • Draw new residues and molecules in a graphical environment
  • View structures graphically
  • Graphically dock molecules
  • Modify the properties of atoms, residues, and molecules using a spreadsheet editor
  • Input or alter molecular mechanics parameters using a spreadsheet editor.
standard amber amino acid residues
“Standard” Amber Amino Acid Residues
  • The N-terminal amino acid names and aliases are prefaced by the letter N (e.g. NALA for N-terminal ALA) and the C-terminal amino acids by the letter C (e.g.CALA)
  • Histidine can exist either as the protonated species or as a neutral species with a hydrogen at the delta or epsilon position. For this reason, the histidine name is either HIP, HID, or HIE (but not HIS). By default LEaP assigns the name HIS to HIE.
  • The AMBER force fields also differentiate between the residue cysteine (CYS) and the similar residue that participates in disulfide bridges, cystine (CYX).
specifying a force field
Specifying a force field
  • There are now a variety of parameterizations, with no obvious "default" value.
  • The "traditional“ parameterization uses fixed partial charges, centered on atoms. Examples of this are ff94, ff99 and ff03
  • The default in versions 8 and 9 of Amber would probably be ff03 or ff99SB, but users should consult the Amber manual
specifying force field in leap
Specifying force field in LEaP

xleap -s -f <filename>

introduction to antechamber
Introduction to Antechamber
  • This is a set of tools to generate files for organic molecules, which can then be read into LEaP.
  • It can perform many file conversions, and can also assign atomic charges and atom types
introduction to sander
Introduction to Sander
  • The acronym stands for Simulated Annealing with NMR-Derived Energy Restraints
  • Sander is the Amber module which carries out energy minimization, molecular dynamics, and NMR refinements.
sander 9 input description
Sander 9 Input Description

sander [-help] [-O] [-A] -i mdin -o mdout

-p prmtop -c inpcrd -r restrt -ref refc

-x mdcrd -y inptraj -v mdvel -e mden

-inf mdinfo -radii radii -cpin cpin

-cpout cpout -cprestrt cprestrt -evbin evbin

Output File

Input File

sander 9 input description for simple runs
Sander 9 Input Description for Simple Runs

sander –O -i mdin -o mdout -p prmtop -c inpcrd

Control data for the minimization/MD run

Molecular topology, force field, periodic box type, atom and residue names

Initial coordinates and (optionally) velocities and periodic box size

preparation of control data for the minimization md run
Preparation of control data for the minimization/MD run

Each of the variables listed below is input in a namelist statement with the namelist identifier &cntrl.

Keyword identifier

End of namelist&cntrl

Variables that are not given in the namelist input retain their default values.

preparation of control data for sander
Preparation of control data for Sander

Toolbar

Option description panel

A Java program has been written to facilitate preparation of input job control files for Sander-8 (support for Sander-9 will be added soon).

It uses intuitive controls to setup job control variables for Sander run. In many cases instead of variable\'s name it uses variable\'s description. For example, for variable NSTLIM it uses "Number of MD Steps (nstlim)".

http://sf.anu.edu.au/~vvv900/cct/appl/sander8input/index.html

preparation of control data for sander1
Preparation of control data for Sander

Closely related options are grouped on separated panels which can be activated using tabs.

Options can be setup using either text fields or combo boxes.

http://sf.anu.edu.au/~vvv900/cct/appl/sander8input/index.html

preparation of control data for sander2
Preparation of control data for Sander

Advanced users might want to edit program options using the built-in text editor, with the program allowing easy switching between GUI and text editing

http://sf.anu.edu.au/~vvv900/cct/appl/sander8input/index.html

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