AMBER - Revision history

Dw34 at 14:22, 7 April 2026

2026-04-07T14:22:58Z

← Older revision		Revision as of 14:22, 7 April 2026
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	* [[Generating parameters using AMBER's built in General Forcefield (gaff)]]		* [[Generating parameters using AMBER's built in General Forcefield (gaff)]]
	* [[Generating parameters using RESP charges from GAMESS-US]]		* [[Generating parameters using RESP charges from GAMESS-US]]
			* [[Building tleap]]
	* [[Simple scripts for LEaP to create topology and coordinate files]]		* [[Simple scripts for LEaP to create topology and coordinate files]]
	* [[Preparing an AMBER topology file for a protein system]] - step by step guide		* [[Preparing an AMBER topology file for a protein system]] - step by step guide

Nn320: /* Tutorials */

2021-10-07T16:00:06Z

Tutorials

← Older revision		Revision as of 16:00, 7 October 2021
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	* [[Simple scripts for LEaP to create topology and coordinate files]]		* [[Simple scripts for LEaP to create topology and coordinate files]]
	* [[Preparing an AMBER topology file for a protein system]] - step by step guide		* [[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		* [[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		* [[Preparing an AMBER topology file for a protein plus ligand system]] - step by step guide

Nn320: /* Tutorials */

2021-10-07T15:51:46Z

Tutorials

← Older revision		Revision as of 15:51, 7 October 2021
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	* [[Simple scripts for LEaP to create topology and coordinate files]]		* [[Simple scripts for LEaP to create topology and coordinate files]]
	* [[Preparing an AMBER topology file for a protein system]] - step by step guide		* [[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		* [[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		* [[Preparing an AMBER topology file for a protein plus ligand system]] - step by step guide

Adk44: Created page with "'''Notes on AMBER 12 interface''' right [http://amber.scripps.edu/ "AMBER"] (Assisted Model Buil..."

2019-05-10T17:03:24Z

Created page with "'''Notes on AMBER 12 interface''' thumb|"The bugs have magically disappeared!"|200px|right [http://amber.scripps.edu/ "AMBER"] (Assisted Model Buil..."

New page

'''[[Notes on AMBER 12 interface]]'''

[[Image:Amberpic.jpg|thumb|"The bugs have magically disappeared!"|200px|right]]
[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].

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]]
* [http://amber.scripps.edu/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 system]] - step by step 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]]