Re: [modeller_usage] loop optimization problem

Hello Modeller Users,

I am trying to run the loop structure refinement using loop_refine.py. I have several 3-5 residue long gaps in my pdb structure and I am trying to get them "patched".

The program crashes with

"..... ddihedr_262E> Central bond too short: 0.000"

I checked the structures (they seem fine) and actually tried running three different loops and the same error pops up.

Would anyone have an idea what the problem is and how I should fix it?

Also: I ran the same time type of calcs with mod8v1 and had no such problems. The only difference is that I switched from Linux to Windows for this run.

tons of thanks for help, Agnieszka