A worldwide e-Infrastructure for NMR and structural biology

Getting started with AMBER

AMBER is a collective name for a suite of programs that allow users to carry out MD simulations on biological systems. The web-portal permits the creation and management of MD calculations from a web browser. The portal takes care also of all the grid accounting. A new user with her/his personal certificate installed in the browser can access to the portal from WeNMR web page and straightforwardly create a new user login and password. The site permits the creation of a new single calculation or the creation of a project where it will be possible to save a number of different calculations that belong to a common project (e.g. MD refinements of protein structures generated with different ensembles of restraints). 

The user can select a pre-set MD refinement protocol to energy optimize NMR protein structures. The currently proposed protocol comprises four steps:

  • In the first step the protein structure to be optimized is uploaded. Here it is possible to upload one pdb file, whose format will be automatically validated and converted into the format recognized by amber. During this step the user can add explicit water molecules to solvate the protein, add counter ions, insert new bonds for selected atoms (e.g. protein to metal). For NMR structures, which are typically represented by a bundle of 20-40 different conformers, this first step is carried out only for the first conformer and then automatically applied to all the structures in the bundle. For each structure in the bundle, an individual job is sent to the grid. 
  • The second step manages the NMR restraints. Four types of restraint are allowed: NOE, dihedral angles, RDCs and pseudocontact shifts (PCS). The last restraints are the so-called paramagnetic restraints. For all restraints it is possible to upload Xplor, Dyana, or Cyana files. For paramagnetic restraints, it is possible to fit the anisotropy tensor directly in the web site.
  • The third step manages the setting of MD calculations. The page can be visualized in a so-called basic mode and in an extended mode, which allows users to view all the details of the amber settings.
  • The fourth and final step allows the user to give a name to the calculation started and submit it to the grid. After the results of a job have been downloaded, the user can browse them and download the various files.

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Cite WeNMR/WestLife

 
Usage of the WeNMR/WestLife portals should be acknowledged in any publication:
 
"The FP7 WeNMR (project# 261572) and H2020 West-Life (project# 675858) European e-Infrastructure projects are acknowledged for the use of their web portals, which make use of the EGI infrastructure and DIRAC4EGI service with the dedicated support of CESNET-MetaCloud, INFN-PADOVA, NCG-INGRID-PT, RAL-LCG2, TW-NCHC, SURFsara and NIKHEF, and the additional support of the national GRID Initiatives of Belgium, France, Italy, Germany, the Netherlands, Poland, Portugal, Spain, UK, South Africa, Malaysia, Taiwan and the US Open Science Grid."
 
And the following article describing the WeNMR portals should be cited:
Wassenaar et al. (2012). WeNMR: Structural Biology on the Grid.J. Grid. Comp., 10:743-767.

EGI-approved

The WeNMR Virtual Research Community has been the first to be officially recognized by the EGI.

European Union

WeNMR is an e-Infrastructure project funded under the 7th framework of the EU. Contract no. 261572

WestLife, the follow up project of WeNMR is a Virtual Research Environment e-Infrastructure project funded under Horizon 2020. Contract no. 675858

West-Life