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 MMMx\example_set. You may want to run and understand demo_Rigi and demo_FlexRNA before and run the demo_RigiFlex over night.

Modules used

Modules Prepare, Rigi, FlexRNA, and YasaraRefine are used.

Functionality

This demo is a pipeline that results from concatenating demo_Rigi and 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 expand RsmE_RsmZ_rba. 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

Outputs are the rigid-body template file RsmE_RsmZ_rigid_bodies.pdb, PDB files of all intermediate models, and the rigid-body arrangement file RsmE_RsmZ_rba.mat.