Distance restraints cause segmentation faults

[Modeller Care <>]

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From: 
Date: Fri, 25 Jul 2003 09:31:27 -0700
To: 
Subject: BOUNCE :    Non-member submission from
["Thorsten Schweikardt" <>]



Dear all,

I am having a problem with the add_restraints-command: using Modeller6v2
(linux/windows-version), I am trying to model the N-terminus of a
protein 
using experimental distance-data. The rest of the protein is available
as
pdb-file and serves as template for the C-terminal end.

Using the linux-version does not work well: without implementing the
distances
or when implementing only the _first_ distance (see below), modeller
works fine, 
but as soon as I want to use another or more than this first distance,
modeller 
crashes with a segmentation fault.

Using the windows-version with the script below, models are produced
that have
an n-terminus formed like a straight line, as if the distance restraints
that
were meant to guide the structure are simply ignored or not read in...

I tried to change the corresponding atoms from 'OG' to 'CA' in case this
option
only works with certain atom types, but this had no effect.

Can someone tell me what I am doing wrong?
 
Many thanks in advance,
Thorsten Schweikardt

Molecular Biophysics
University of Mainz


Top-File:
-----------------------------
INCLUDE
SET ALNFILE = 'alignment.ali'
SET KNOWNS = 'protein1'
SET SEQUENCE = 'protein1plusnterm'
SET ATOM_FILES_DIRECTORY = './'
SET STARTING_MODEL= 1
SET ENDING_MODEL = 20

SET LIBRARY_SCHEDULE = 4
SET FINAL_MALIGN3D = 1
CALL ROUTINE = 'model'

SUBROUTINE ROUTINE = 'special_restraints'
SET ATOM_IDS = 'OG:3' 'OG:169'
ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 30.0 10.0
SET ATOM_IDS = 'OG:116' 'OG:169'
ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 40.0 0.0
SET ATOM_IDS = 'CA:42' 'CA:169'
ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 40.0 1.0
SET ATOM_IDS = 'CA:3' 'CA:42'
ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 21.0 4.0
SET ATOM_IDS = 'CA:3' 'CA:116'
ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 50.0 1.0
RETURN
END_SUBROUTINE



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