Analysing an active site


Building Loops


Building a functionnal unit from a monomer


Crystal Symmetries


Electron Density Maps


Energy minimisation


Fitting Residues into Electron Density


Homology modelling


Making Phi/Psi statistics


Superposing Proteins





Last modified
31 March 98
by N.Guex


Energy Minimisation

Swiss-PdbViewer cannot perform energy minimisation by itself. However, it is possible to prepare command files to do energy minimisation through external programs such as CHARMm, AMBER, or GROMOS running under Unix.


The material provided below assumes that you run your external program on a SGI computer, with a c-shell, and that perl is installed on your system. However, it shouldn't be difficult to modify the scripts to run on other computers.

  • First of all, add this to your .cshrc

Then, download the perl script that will launch your energy favourite energy minimizer.

Now read the important information and do the tutorial corresponding to your energy minimizer.