  We consider self-assembly of proteins into a virus capsid by the methods of
molecular dynamics. The capsid corresponds either to SPMV or CCMV and is
studied with and without the RNA molecule inside. The proteins are flexible and
described by the structure-based coarse-grained model augmented by
electrostatic interactions. Previous studies of the capsid self-assembly
involved solid objects of a supramolecular scale, e.g. corresponding to
capsomeres, with engineered couplings and stochastic movements. In our
approach, a single capsid is dissociated by an application of a high
temperature for a variable period and then the system is cooled down to allow
for self-assembly. The restoration of the capsid proceeds to various extent,
depending on the nature of the dissociated state, but is rarely complete
because some proteins depart too far unless the process takes place in a
confined space.
