I did some tests and realized that the segmentation fault occurs when calling the methods ShearMover or FragmentMover. When I use only the methods SmallMover, RigidBodyPerturbMover, RigidBodySpinMover, DockingLowRes and DockingHighRes the script works normally. But I still can not find the reason, because in another script ShearMover method works well.
For some reason still can not explain I changed my input pdb file. That has had a metal atom at the beginning of the sequence used in movemap, causing the error when I called fragmentmover or shearmover. Now I fix my pdb file and everything’s back to work.