Hello, I’ve been using the Macromolecular Coarse-Grained Flexibility workflow ( Jupyter Notebook Macromolecular Coarse-Grained Flexibility tutorial ) with an api.alphafold module. My main problem is that the Brownian dynamics simulation stopped working, giving me a bd_ensemble.mdcrd output that is either empty or just filled with “NaN”. The ca.pdb file is fine and the other simulations (dmd and nma) are running perfectly. Could the problem be that the distance in Angstrom between the alpha carbons is too short? If so, how can this be solved? Thanks in advance!!
Hi Giulya,
the point here is that BioBB is just wrapping already existing tools. In this case, the problem is given by the BD tool, and not the wrapper by itself. In any case, we could try to explore what can be causing the problem if you send us the PDB you are using as an input.
If you are interested in generating ensembles out of a structure, you can also explore the “Protein conformational ensembles generation” workflow from our collection here: Workflows - BioExcel Building Blocks . This one contains more tools to generate ensembles such as concoord, imods, prody and nolb.
Hope this helps!