Subject: Re: [modeller_usage] loop optimization problem
From: Modeller Caretaker <>
Date: Wed, 07 Jun 2006 18:37:16 -0700
Cc:
Agnieszka Szarecka wrote:
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"
This means that Modeller was unable to calculate the derivatives of a
dihedral feature because the distance between the two central atoms in
the dihedral became too short, leading to numerical instability. In this
case, the distance is zero, meaning that the two atoms are on top of
each other. This can happen if for some reason there's a strong
attractive interaction between two atoms. You don't have electrostatics
turned on, do you?
Would anyone have an idea what the problem is and how I should fix it?
If you make no progress, tar up your input files and send them to me,
and I'll take a look.
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.
The final structures you get are strongly dependent on the initial,
randomized, coordinates. These differ between operating systems and
Modeller versions due to differences in the representation and rounding
of floating point numbers.