From: Rune Thomas Kidmose (
Date: Mon Mar 12 2018 - 09:14:32 CDT


Basically I would like to know, if it is possible to run a MDFF simulation on a whole 70S ribosome at once?

I have only been able to do it on the LSU and then on the SSU separately, due to the constraints of the PDB format regarding unique chain ID's. Afterwards I then combine the two trajectories for visualization purposes only.

Obviously the way I do it, the LSU does not feel or know anything about the SSU and vice versa.

But I was wondering if it is possible to supply MDFF with multiple PSF and PDB files and multiple gridpdb files as well, but only one gridmap, which could then enable running MDFF on a whole ribosome at once.

I have played around a bit with it, but I have not been able to make MDFF accept multiple PSF and PDB files.