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AMBER  
 
AMBER
Description 
Amber is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations, particularly on biomolecules. None of the individual programs carries this name, but the various parts work reasonably well together, and provide a powerful frame- work for many common calculations. The term amber is also sometimes used to refer to the empirical force fields that are implemented here. It should be recognized however, that the code and force field are separate: several other computer packages have implemented the amber force fields, and other force fields can be implemented with the amber programs. Fur- ther, the force fields are in the public domain, whereas the codes are distributed under a license agreement.

The Amber software suite is divided into two parts: AmberTools, a collection of freely avail- able programs mostly under the GPL license, and Amber11, which is centered around the sander and pmemd simulation programs, and which continues to be licensed as before, under a more restrictive license. You need to install both parts, starting with AmberTools.

Amber 11 (2010) represents a significant change from the most recent previous version, Amber 10, which was released in April, 2008. Please refer to the official homepage for an overview of the most important changes. 

Official Homepage
 
Documentation
Users Manual
  1. Amber 11 User Manual (PDF)
  2. AmberTools 1.5 User Manual (PDF)
  3. Corrections of the Manuals (On-line)

Other References
  1. 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).
  2. 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).
License Agreement and Citation Format
License Agreement
Commercial License

Citation Format 
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, B. Wang, S. Hayik, A. Roitberg, G. Seabra, I. Kolossvai, K.F. Wong, F. Paesani, J. Vanicek, 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, C. Sagui, V. Babin, T. Luchko, S. Gusarov, A. Kovalenko, and P.A. Kollman (2010), AMBER 11, University of California, San Francisco.
 
How to Access the Program 
 
Availability
Servers Versions Paths Parallelization Methods
Fuji 11 /apps/Amber/amber11 MPI
Axle 9 /apps/Amber/amber9 MPI
10 /apps/Amber/amber10 MPI
11 /apps/Amber/amber11 MPI, CUDA
Using the Program
 
Additional Notes
 
Last Updated - 4th Oct 2011
 
     
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