Re: [modeller_usage] loop optimization problem

[Agnieszka Szarecka <szarecka+ AT pitt.edu>]

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