Run it by typing
MMMx demo_RigiFlex. This example generates logfile
demo_RigiFlex.log. The logfile is automatically displayed after completion by the
#report directive at the end.
Note that this demo runs for a long time and creates a sizeable ensemble. Therefore, it is contained in a separate subdirectory of
You may want to run and understand
demo_FlexRNA before and run the
demo_RigiFlex over night.
YasaraRefine are used.
This demo is a pipeline that results from concatenating
demo_FlexRNA. Please consult the documentation of these two parts for a description of functionality.
The only change required for concatenation concerns the first
FlexRNA call, where the input statement
addpdb RsmE_RsmZ_rigid_bodies is replaced by
The new input statement expands the rigid-body output of
Rigi to PDB files. The
FlexRNA calls are written in a way that they operate on the whole ensemble.
Ensemble size reduces between these calls, since some of the rigid-body arrangements cannot be connected by (all) RNA linkers.
Outputs are the rigid-body template file
RsmE_RsmZ_rigid_bodies.pdb, PDB files of all intermediate models, and the rigid-body arrangement file