I've successfully run Rosetta Design using the April 14th, 2014 weekly release (this is the latest weekly release that I can faithfully use, given the age of our cluster) on a large number of scaffolds. I've attached the options file (femoco2.txt) as a reference.
However, after generating scorefiles for my designs, I've run into an issue where some of the rows have negative values for the SR_3_hbond_pm column, which misaligns everything and makes it so I can't run DesignSelect.py to rank or sort my results because the number of columns is not the same. I've attached a .txt file containing the offending rows (in this case, rows 86-88).
Is this an issue with my Design run, or just those specific input pbds? Is there a way I can remove these automatically (there are quite a few in my full run, so doing it manually would be arduous).