Subject: Re: [modeller_usage] loop optimization problem
From: Agnieszka Szarecka <szarecka+@pitt.edu>
Date: Wed, 07 Jun 2006 11:08:49 -0400 (EDT)
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.