Difference between revisions of "AMBER"
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[[Image:Amberpic.jpg|thumb|"The bugs have magically disappeared!"|200px|right]] |
[[Image:Amberpic.jpg|thumb|"The bugs have magically disappeared!"|200px|right]] |
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| − | + | [http://amber.scripps.edu/ "AMBER"] (Assisted Model Building with Energy Refinement) 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. We mainly use the MM forcefields interfaced with other group software i.e. [[GMIN]] or [[OPTIM]]. The included programmes such as ''sander'' and ''antechamber'' are however, extremely useful in some circumstances! The full user manual for AMBER9 can be found in pdf format [http://amber.scripps.edu/doc9/amber9.pdf here]. |
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== Tutorials == |
== Tutorials == |
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Revision as of 19:53, 15 May 2008
"AMBER" (Assisted Model Building with Energy Refinement) 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. We mainly use the MM forcefields interfaced with other group software i.e. GMIN or OPTIM. The included programmes such as sander and antechamber are however, extremely useful in some circumstances! The full user manual for AMBER9 can be found in pdf format here.
Tutorials
- Ross Walker's AMBER9 tutorials - recommended reading for ANYONE using AMBER!
- Generating parameters using AMBER's built in General Forcefield (gaff)
- Generating parameters using RESP charges from GAMESS-US
- Simple scripts for LEaP to create topology and coordinate files
- Preparing an AMBER topology file for a protein plus ligand system - step by step guide
- Running MD with AMBER