Amber

From Biowerkzeug Wiki

Amber (Assisted Model Building with Energy Refinement) refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules [1, 2] (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs [3] which includes source code and demos. The current version of the code is Amber version 10, which is distributed by UCSF subject to a licensing agreement.

Amber is now distributed in two parts: AmberTools and Amber10. You can use AmberTools without Amber10, but not vice versa.

Documentation

Tutorials

• Beginners' and Advanced Tutorials

References

1. Ponder JW and Case DA. Force fields for protein simulations. Adv Protein Chem 2003; 66 27-85. pmid:14631816. PubMed HubMed [Ponder2003]
2. Cheatham TE 3rd and Young MA. Molecular dynamics simulation of nucleic acids: successes, limitations, and promise. Biopolymers 2000-2001; 56(4) 232-56. doi:10.1002/1097-0282(2000)56:4<232::AID-BIP10037>3.0.CO;2-H pmid:11754338. PubMed HubMed [Cheatham2001]
3. Case DA, Cheatham TE 3rd, Darden T, Gohlke H, Luo R, Merz KM Jr, Onufriev A, Simmerling C, Wang B, and Woods RJ. The Amber biomolecular simulation programs. J Comput Chem 2005 Dec; 26(16) 1668-88. doi:10.1002/jcc.20290 pmid:16200636. PubMed HubMed [Case2005]

All Medline abstracts: PubMed HubMed