AMBER

Notes on AMBER 12 interface

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"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.

As of July 2009, the SVN repository also contains AMBER Tools, the stand alone suite of programs that generate AMBER input files and allow you to analyse output. You can find a manual within the repository. Look in AMBERTOOLS/doc.

Tutorials

• Using AMBER 14 on the GPU and compute clusters
• 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 system - step by step guide
• Preparing input files for a peptide using AMBER - detailed guide
• Setting up - step by step guide to prepare and then symmetrise a simple (protein-only) system
• Preparing an AMBER topology file for a protein plus ligand system - step by step guide
• Symmetrising AMBER topology files - step by step guide for symmetrising a complex protein+ligand system
• Producing a PDB from a coordinates and topology file - using amdpdb
• Running GMIN with MD move steps AMBER
• Evaluating different components of AMBER energy function with SANDER
• Running MD with AMBER
• Running MD on GPUS with pmemd_cuda
• REMD with AMBER
• Performing a hydrogen-bond analysis