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).

Required Modules

For more details on specific modules required for different versions of AMBER, run module spider amber

Serial For Amber 18: intel/2017 amber/18 For amber 16: intel/2018.1.163 amber Example: module load intel/2017 amber/18

Parallel (MPI) For amber 18 intel/2017 openmpi/3.1.2 amber/18 For amber/16: intel/2018.1.163 openmpi/3.0.0 amber Example: module load intel/2017 openmpi/3.1.2 amber/18

GPU (Parallel/MPI) For amber 18: cuda/9.2.88 intel/2017 openmpi/3.1.2 amber/18 Example: module load cuda/9.2.88 intel/2017 openmpi/3.1.2 amber/18

System Variables

• AMBERHOME
• HPC_AMBER_DIR - installation directory
• HPC_AMBER_BIN - executable program directory
• HPC_AMBER_LIB - library directory
• HPC_AMBER_INC - include file directory

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.