Team:EPF-Lausanne/Implementation

LOV domains are the light-sensitive portion of phototropins. They absorb light through a flavin cofactor, photo-chemicaly form a covalent bond between the chromophore and a cysteine residue in the protein, and proceed to mediate activation of an attached kinase domain.

Generating input files

First we need a compatible .pdb in addition to parameter and topology files. Steps to generate all the input files are explained in detail on this page How to generate input files. This is a kind of summary of the tuto.

.conf parameters

We should explain here what are the keywords we use in the .conf.

Run a complete simulation

We start from .pdb, .psf, .rtf generated in the previous section. Complete process is on a separate page How to run a simulation.