| Name: |
Amber |
| Version(s): |
8.0, 7.0, 4.1 (versions 4.1 only under SGI Irix)
|
| Category: |
Molecular Modeling; XRay/NMR Structure Refinement; Molecular Visualization
|
| Author(s)/Vendor(s): |
David A. Case, David A. Pearlman, James W. Caldwell,
T.E. Cheatham III, Carlos Simmerling, Peter A. Kollman
and many others
|
| Program Description: |
AMBER-Assisted Model Building with Energy Refinement
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 program carries this name, but the various parts work
reasonably well together, and
provide a powerful framework for
many common calculations.
The term amber is also sometimes used to refer to the empirical force fields
that are implemented in AMBER. It should be recognized that the code and the force
fields are separate: several other computer packages have implemented the
amber force fields, and other force fields can be implemented with the amber
program. Further, the force fields are in the public domain, whereas the codes are
distributed under a license agreement.
|
| Computer platform(s): |
SGI-MIPS (Irix), SGI-Altix (Linux-64), Linux, IBM AIX
|
| Location: |
/usr/local/fbscapp/amber8
/usr/local/fbscapp/amber7
/usr/local/fbscapp/amber6
/usr/local/fbscapp/amber4.1
(the last two only under SGI-Irix)
|
| Access: |
An account at ABCC is needed to use AMBER.
AMBER8
-------
setenv AMBERHOME /usr/local/fbscapp/amber8
set path = ($AMBERHOME $AMBERHOME/exe)
AMBER 7
-------
setenv AMBERHOME /usr/local/fbscapp/amber7
set path = ($AMBERHOME $AMBERHOME/exe)
Note, that any CPU-intensive calculations must be executed in the batch mode. |
| Documentation: |
AMBER8
-------
/usr/local/fbscapp/amber8/doc
http://www.abcc.ncifcrf.gov/SciApps/Docs/AMBER8
AMBER 7
-------
/usr/local/fbscapp/amber7/doc/amber7.pdf
AMBER 6
-------
/usr/local/fbscapp/amber6/doc/amber6.pdf
|
| Web Site: |
http://amber.scripps.edu/
|
| ABCC Contact Person: |
Karol Miaskiewicz (or)
Sarangan Ravichandran
|
| Created By: |
ravichas |
| Created Time: |
2002-07-01 |
| Updated By: |
miaskiew
|
| Updated Time: |
2004-07-29 |
