Hello, I would like to apply rigid bodies only on the mainchain of my model in order to run molecular dynamics and conjuguate gradients. I have already tried to do it with :
mdl.restraints.rigid_bodies.append(rigid_body(mdl.residue_range('56:A', '48:A')))
and just before the optimization start :
atmselall = selection(mdl) atmsel = selection.only_mainchain(atmselall)
and then :
cg.optimize(atmsel, max_iterations=50, actions=actions.trace(5, trcfil))
But my model is destroyed by CG and MD which is not the case when rigid body is applied on the whole chain.
Maybe I can define "rigid_body" with "atom_range" in place of "residue_range" and selecting all the atoms of the backbone (Ca, CO, N) for my residue range, but I think there must be a better way to achieve this. Many Thanks for any suggestion.
Depret Grégoire Graduate Student
gdepret@ulb.ac.be Service de Structure et Fonction des Membranes Biologiques Centre de Biologie Structurale et de Bioinformatique Université Libre de Bruxelles Boulevard du Triomphe CP 206/2 B-1050 Bruxelles Belgium