Difference between revisions of "AMBER"
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* [[Producing a PDB from a coordinates and topology file]] - using ''amdpdb'' |
* [[Producing a PDB from a coordinates and topology file]] - using ''amdpdb'' |
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* [[Preparing an AMBER topology file for a protein plus ligand system]] - step by step guide |
* [[Preparing an AMBER topology file for a protein plus ligand system]] - step by step guide |
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| + | * [[Running GMIN with MD move steps AMBER]] |
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* [[Running MD with AMBER]] |
* [[Running MD with AMBER]] |
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* [[REMD with AMBER]] |
* [[REMD with AMBER]] |
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Revision as of 12:52, 28 July 2009
"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
- Producing a PDB from a coordinates and topology file - using amdpdb
- Preparing an AMBER topology file for a protein plus ligand system - step by step guide
- Running GMIN with MD move steps AMBER
- Running MD with AMBER
- REMD with AMBER