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       home 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. script for CHARMm script for AMBER script for GROMOS Now read the important information and do the tutorial corresponding to your energy minimizer. tutorial for CHARMm tutorial for AMBER tutorial for GROMOS