4 Nov
2020
4 Nov
'20
3:58 p.m.
On 11/4/20 6:01 AM, Altair Hernández wrote: > I am trying to sample a PDB with different restraints. I would like to > shuffle only some molecules, in order to have some of them in a fixed > position (the coordinates should not change after sampling). I define > these rigid particles as rigid bodies before shuffling
A rigid body is not fixed in space - it is merely constrained to move rigidly. But excluded_rigid_bodies should prevent shuffle_configuration from modifying those rigid bodies. My guess is that your 'fixed_particles' isn't really a list of RigidBody objects and so isn't matching anything. I can't say for sure though without seeing a complete working script.
Ben
--
ben@salilab.org https://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
- Sir Arthur Conan Doyle