A short introduction to the AMBER service
AMBER is a suite of software for simulation of biomolecule dynamics. The website portal allows users to build and manage molecular dynamics simulations via their web browser while tracking the computational status of the grid.
New users need to install their personal certificate in the browser. Then, by logging from the WeNMR gateway page it is possible to directly create a new user account and password for the AMBER portal. The AMBER portal allows users to set up a new calculation through several different protocols
A main application is molecular dynamics refinement of protein structures derived from NMR restraints. For this, the currently recommended method consists of four steps: First, upload the protein structure that needs to be optimized. You can upload the pdb file, AMBER will automatically review and convert it into a format that AMBER can read. In this step, the user can add water molecules, anti-ions or on selected atoms Embedding new bonds (such as proteins linked to metal) for nuclear magnetic resonance structures, usually 20-40 different configurations, this step only for the first configuration, and then applied in all configurations, each structure In the grid are independent of the operation It is possible to use four types of distance limits: NOE, dihedral angles, RDC and PCS. The last one is the so-called paramagnetic distance limit. The distance limit can be uploaded to Xplor, Dyana, or Cyana format files Paramagnetic limitations can be fitted directly to an anisotropic tensor on a website. Users can submit jobs to the grid and track their status.
The portal can be accessed here.