Scientific Application – Amber

Table of Contents

Overview

Setting up your Environment and Invoking

Notes

Links

Recommended Citations

Additional Help

Overview

Amber (Assisted Model Building with Energy Refinement) is a general-purpose molecular mechanics and dynamics program designed for the refinement of macro-molecular conformations using an analytical potential energy function. All Amber modules execute on our support servers. The program includes molecular dynamics, energy minimization (MIN), normal mode analysis (NMODE), Gibbs free energy perturbation modules, and structure refinement using information from NMR spectroscopy as constraints (Sander).

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.

The release consists of about 60 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.
  • Gibbs: This program includes free energy perturbation (FEP) and thermodynamic integration (TI) [window growth, slow growth, and dynamically modified windows], and also allows potential of mean force (PMF) calculations.
  • 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. Motif-style X-windows Athena widgets and a table widget used in LEaP were written by Vladimir Romanovski.
  • Interface: Interface is a scripting language that can be used for running Sander and Gibbs with higher-level input specifications. It includes various intrinsic functions such as DO-loops, IF and GOTO constructs, variable assignment statements, numerous functions (e.g. SIN, COS, EXP, etc.), and in-line variable substitution. Thus, one can run numerous Amber jobs from one script, changing only desired elements of the simulation for each run. For example, one might define a torsional restraint whose target value changed on each iteration of a DO-loop. This makes it easy to perform torsional driving, for example.

 

Research Computing Server(s): Kure/Killdevil
Default Version: 12p19 (Kure/Killdevil)
Installed Version(s): 11p19, 11p22, 12p7, 12p13, 12p19

Setting up your Environment and Invoking

Amber can be accessed through the Research Computing servers KillDevil and Kure. Sander is one of the major applications in the Amber package. Since Sander is capable of running in parallel, it is advisable to run Sander jobs on the Research Computing servers KillDevil.

module add amber

Notes

  • Amber can be installed locally on UNC machines running UNIX operating systems as specificed in the Amber 9 License Agreement. This software can be acquired through the UNC package (pkg) space as follows:

1. Access UNC AFS space through use of an AFS client or through one of the ITS servers connected to UNC AFS space, such as the Isis system or Research Computing servers.

2. Switch to the directory: /afs/isis/pkg/amber-9p139/dist

3. In this directory, the files amber9.tgz, mview102.tgz, tutorial.tgz and readme.txt all need to be copied to the local computer. These are the necessary installation files that come from the Amber 9 disk distributed to UNC.

4. The readme.txt file details how to setup, install and run Amber on a local computer using the three *.tgz files downloaded from the pkg space.

5. Amber can then be installed locally on UNC machines or personal computers of UNC researchers who will be using the software for research performed at UNC (as detailed by the Amber 9 License Agreement).

Links

Recommended Citations

  • When citing Amber 8 in the literature, the following citation should be used:
  • D.A. Case, T.A. Darden, T.E. Cheatham, III, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, K.M. Merz, B. Wang, D.A. Pearlman, M. Crowley, S. Brozell, V. Tsui, H. Gohlke, J. Mongan, V. Hornak, G. Cui, P. Beroza, C. Schafmeister, J.W. Caldwell, W.S. Ross, and P.A. Kollman (2004), AMBER 8, University of California, San Francisco.
  • When citing Amber 9 in the literature, the following citation should be used:
  • D.A. Case, T.A. Darden, T.E. Cheatham, III, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, K.M. Merz, D.A. Pearlman, M. Crowley, R.C. Walker, W. Zhang, B. Wang, S. Hayik, A. Roitberg, G. Seabra, K.F. Wong, F. Paesani, X. Wu, S. Brozell, V. Tsui, H. Gohlke, L. Yang, C. Tan, J. Mongan, V. Hornak, G. Cui, P. Beroza, D.H. Mathews, C. Schafmeister, W.S. Ross, and P.A. Kollman (2006), AMBER 9, University of California, San Francisco.
  • The history of the codes and a basic description of the methods can be found in the following two papers:
  • D.A. Pearlman, D.A. Case, J.W. Caldwell, W.S. Ross, T.E. Cheatham, III, S. DeBolt, D. Ferguson, G. Seibel, and P.Kollman. AMBER, a package of computer programs for applying molecular meechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Comp. Phys. Commun. 91, 1-41 (1995).
  • D.A. Case, T. Cheatham, T. Darden, H. Gohlke, R. Luo, K.M. Merz, Jr., A. Onufriev, C. Simmerling, B. Wang and R. Woods. The Amber biomolecular simulation programs. J. Computat. Chem. 26, 1668-1688 (2005).

Additional Help

Research Computing home pageĀ