TUTORIAL

 

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

 

 

 

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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.


Requirements

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.