AMBER

Description

Amber website  

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.

A good general overview of the Amber codes can be found in: D.A. Case, T.E. Cheatham, III, 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).

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).

Version Note

The default version of Amber is Amber 12. Amber 11 is also available via module load amber/11. If you are still using Amber 11, you should switch to Amber 12 as soon as you can.

This installation has bugfixes up to 13 for Amber12 and 29 for AmberTools.

Required Modules

Serial

• intel
• amber

Parallel (MPI)

• intel
• openmpi
• amber

GPU (Serial)

• intel
• cuda/4.2
• amber

GPU (Parallel/MPI)

• intel
• openmpi
• cuda/4.2
• amber

System Variables

• AMBERHOME

PBS Script Examples

See the AMBER_PBS page for Amber PBS script examples.

Citation

Serial Version

If you publish research that uses Amber you have to cite it as follows:
D.A. Case, T.A. Darden, T.E. Cheatham, III, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, R.C. Walker, W. Zhang, K.M. Merz, B. Roberts, S. Hayik, A. Roitberg, G. Seabra, J. Swails, A.W. Goetz, I. Kolossvai, K.F. Wong, F. Paesani, J. Vanicek, R.M. Wolf, J. Liu, X. Wu, S.R. Brozell, T. Steinbrecher, H. Gohlke, Q. Cai, X. Ye, J. Wang, M.-J. Hsieh, G. Cui, D.R. Roe, D.H. Mathews, M.G. Seetin, R. Salomon-Ferrer, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko, and P.A. Kollman (2012), AMBER 12, University of California, San Francisco.

GPU Version

If you make use of any of this GPU support in your work please use the following citations:

Andreas W. Goetz; Mark J. Williamson; Dong Xu; Duncan Poole; Scott Le Grand; & Ross C. Walker* "Routine microsecond molecular dynamics simulations with AMBER - Part I: Generalized Born", J. Chem. Theory Comput., 2012, 8 (5), pp 1542-1555 , DOI: 10.1021/ct200909j

D.A. Case, T.A. Darden, T.E. Cheatham, III, C.L. Simmerling, J. Wang, R.E. Duke, R. Luo, R.C. Walker, W. Zhang, K.M. Merz, B. Roberts, S. Hayik, A. Roitberg, G. Seabra, J. Swails, A.W. Goetz, I. Kolossvai, K.F. Wong, F. Paesani, J. Vanicek, R.M. Wolf, J. Liu, X. Wu, S.R. Brozell, T. Steinbrecher, H. Gohlke, Q. Cai, X. Ye, J. Wang, M.-J. Hsieh, G. Cui, D.R. Roe, D.H. Mathews, M.G. Seetin, R. Salomon-Ferrer, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko, and P.A. Kollman (2012), AMBER 12, University of California, San Francisco.