Difference between revisions of "AMBER"
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| − | "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. |
+ | "AMBER" (homepage [http://amber.scripps.edu/ here]) 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 i.e. ''sander'' and ''antechamber'' are however, extremely useful in some circumstances! |
== Tutorials == |
== Tutorials == |
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| + | * [http://amber.scripps.edu/tutorials/ Ross Walker's AMBER9 tutorials] - recommended reading for '''ANYONE''' using AMBER! |
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* [[Preparing an AMBER topology file for a protein plus ligand system]] - step by step |
* [[Preparing an AMBER topology file for a protein plus ligand system]] - step by step |
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Revision as of 15:19, 12 May 2008
"AMBER" (homepage here) 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 i.e. sander and antechamber are however, extremely useful in some circumstances!
Tutorials
- Ross Walker's AMBER9 tutorials - recommended reading for ANYONE using AMBER!
- Preparing an AMBER topology file for a protein plus ligand system - step by step