Dear Edward, find the log file after i run the script dauvergne_protocol using my values
Hope this helps you understand my problem about vectors.
relax 1.3.16
Molecular dynamics by NMR data analysis
Copyright (C) 2001-2006 Edward d'Auvergne
Copyright (C) 2006-2012 the relax development team
This is
free software which you are welcome to modify and redistribute under
the conditions of the GNU General Public License (GPL). This program,
including all modules, is licensed under the GPL and comes with absolutely no
warranty. For details type 'GPL' within the relax prompt.
Assistance in using the relax prompt and scripting interface can be accessed by
typing 'help' within the prompt.
Processor fabric: Uni-processor.
script =
'dauvergne_protocol.py'
----------------------------------------------------------------------------------------------------
###############################################################################
# #
# Copyright (C) 2004-2012 Edward d'Auvergne
#
# #
# This file is part of the program relax.
#
# #
# relax is free software; you can redistribute it and/or modify #
# it under the terms of the GNU General Public License as published by #
# the Free Software Foundation; either version 2 of the License, or #
# (at your option) any later
version. #
# #
# relax is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty
of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# #
# You should have
received a copy of the GNU General Public License #
# along with relax; if not, write to the Free Software #
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA #
#
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###############################################################################
"""Script for black-box model-free analysis.
This script is designed for those who appreciate black-boxes or those who appreciate complex code. Importantly data at multiple magnetic field strengths is essential for this analysis. The script will need to be heavily tailored to the molecule in question by changing the variables just below this documentation. If you would like to change how model-free analysis is performed, the code in the class Main can be changed as needed. For a description of object-oriented coding in python using classes, functions/methods, self, etc., see the python tutorial.
If you have obtained this script without the program relax, please visit http://www.nmr-relax.com.
References
==========
The model-free optimisation methodology herein is that of:
d'Auvergne, E. J. and Gooley, P. R. (2008b). Optimisation of NMR dynamic models II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor. J. Biomol. NMR, 40(2), 121-133
Other references for features of this script include model-free model selection using Akaike's Information Criterion:
d'Auvergne, E. J. and Gooley, P. R. (2003). The use of model selection in the model-free analysis of protein dynamics. J. Biomol. NMR, 25(1), 25-39.
The elimination of failed model-free models and Monte Carlo simulations:
d'Auvergne, E. J. and Gooley, P. R. (2006). Model-free model elimination: A new step in the model-free dynamic analysis of NMR relaxation data. J. Biomol. NMR, 35(2), 117-135.
Significant model-free optimisation improvements:
d'Auvergne, E. J. and Gooley, P. R. (2008a). Optimisation of NMR
dynamic models I. Minimisation algorithms and their performance within the model-free and Brownian rotational diffusion spaces. J. Biomol. NMR, 40(2), 107-109.
Rather than searching for the lowest chi-squared value, this script searches for the model with the lowest AIC criterion. This complex multi-universe, multi-dimensional search is formulated using set theory as the universal solution:
d'Auvergne, E. J. and Gooley, P. R. (2007). Set theory formulation of the model-free problem and the diffusion seeded model-free paradigm. 3(7), 483-494.
The basic three references for the original and extended model-free theories are:
Lipari, G. and Szabo, A. (1982a). Model-free approach to the interpretation of nuclear magnetic-resonance relaxation in macromolecules I. Theory and range of validity. J. Am. Chem. Soc., 104(17), 4546-4559.
Lipari, G. and Szabo, A.
(1982b). Model-free approach to the interpretation of nuclear magnetic-resonance relaxation in macromolecules II. Analysis of experimental results. J. Am. Chem. Soc., 104(17), 4559-4570.
Clore, G. M., Szabo, A., Bax, A., Kay, L. E., Driscoll, P. C., and Gronenborn, A.M. (1990). Deviations from the simple 2-parameter model-free approach to the interpretation of N-15 nuclear magnetic-relaxation of proteins. J. Am. Chem. Soc., 112(12), 4989-4991.
How to use this script
======================
The value of the variable DIFF_MODEL will determine the behaviour of this script. The five diffusion models used in this script are:
Model I (MI) - Local tm.
Model II (MII) - Sphere.
Model III (MIII) - Prolate spheroid.
Model IV (MIV) - Oblate spheroid.
Model V (MV) - Ellipsoid.
Model I must be optimised prior to any of the other diffusion models, while the Models II to V can be optimised in any order. To select the various models, set the variable DIFF_MODEL to the following strings:
MI - 'local_tm'
MII - 'sphere'
MIII - 'prolate'
MIV - 'oblate'
MV - 'ellipsoid'
This approach has the advantage of eliminating the need for an initial estimate of a global diffusion tensor and removing all the problems associated with the initial estimate.
It is important that the number of parameters in a model does not exceed the number of relaxation data sets for that spin. If this is the case, the list of models in the MF_MODELS and LOCAL_TM_MODELS variables will need to be trimmed.
Model I - Local
tm
~~~~~~~~~~~~~~~~~~
This will optimise the diffusion model whereby all spin of the molecule have a local tm value, i.e. there is no global diffusion tensor. This model needs to be optimised prior to optimising any of the other diffusion models. Each spin is fitted to the multiple model-free models separately, where the parameter tm is included in each model.
AIC model selection is used to select the models for each spin.
Model II - Sphere
~~~~~~~~~~~~~~~~~
This will optimise the isotropic diffusion model. Multiple steps are required, an initial optimisation of the diffusion tensor, followed by a repetitive optimisation until convergence of the diffusion tensor. Each of these steps requires this script to be rerun. For the initial optimisation, which will be placed in the directory './sphere/init/', the following steps are used:
The model-free models and parameter values for each spin
are set to those of diffusion model MI.
The local tm parameter is removed from the models.
The model-free parameters are fixed and a global spherical diffusion tensor is minimised.
For the repetitive optimisation, each minimisation is named from 'round_1' onwards. The initial 'round_1' optimisation will extract the diffusion tensor from the results file in './sphere/init/', and the results will be placed in the directory './sphere/round_1/'. Each successive round will take the diffusion tensor from the previous round. The following steps are used:
The global diffusion tensor is fixed and the multiple model-free models are fitted to each spin.
AIC model selection is used to select the models for each spin.
All model-free and diffusion parameters are allowed to vary and a global optimisation of all parameters is carried out.
Model III - Prolate
spheroid
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
The methods used are identical to those of diffusion model MII, except that an axially symmetric diffusion tensor with Da >= 0 is used. The base directory containing all the results is './prolate/'.
Model IV - Oblate spheroid
~~~~~~~~~~~~~~~~~~~~~~~~~~
The methods used are identical to those of diffusion model MII, except that an axially symmetric diffusion tensor with Da <= 0 is used. The base directory containing all the results is './oblate/'.
Model V - Ellipsoid
~~~~~~~~~~~~~~~~~~~
The methods used are identical to those of diffusion model MII, except that a fully anisotropic diffusion tensor is used (also known as rhombic or asymmetric diffusion). The base directory is './ellipsoid/'.
Final run
~~~~~~~~~
Once all the diffusion models have converged, the final run can be executed. This is done by setting
the variable DIFF_MODEL to 'final'. This consists of two steps, diffusion tensor model selection, and Monte Carlo simulations. Firstly AIC model selection is used to select between the diffusion tensor models. Monte Carlo simulations are then run solely on this selected diffusion model. Minimisation of the model is bypassed as it is assumed that the model is already fully optimised (if this is not the case the final run is not yet appropriate).
The final black-box model-free results will be placed in the file 'final/results'.
"""
# Python module imports.
from time import asctime, localtime
# relax module imports.
from auto_analyses.dauvergne_protocol import dAuvergne_protocol
# Analysis variables.
#####################
# The diffusion model.
DIFF_MODEL = 'local_tm'
# The model-free models. Do not change these unless absolutely necessary, the protocol is likely to
fail if these are changed.
MF_MODELS = ['m0', 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9']
LOCAL_TM_MODELS = ['tm0', 'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6', 'tm7', 'tm8', 'tm9']
# The grid search size (the number of increments per dimension).
GRID_INC = 11
# The optimisation technique.
MIN_ALGOR = 'newton'
# The number of Monte Carlo simulations to be used for error analysis at the end of the analysis.
MC_NUM = 500
# Automatic looping over all rounds until convergence (must be a boolean value of True or False).
CONV_LOOP = True
# Set up the data pipe.
#######################
# The following sequence of user function calls can be changed as needed.
# Create the data pipe.
name = "mf (%s)" % asctime(localtime())
pipe.create(name, 'mf')
# Load the sequence.
sequence.read(file='noe.600.out', dir=None, mol_name_col=None, res_num_col=1, res_name_col=2,
spin_num_col=None, spin_name_col=None)
# Name the spins.
spin.name(name='N')
# Load the PDB file.
structure.read_pdb('rS2.pdb')
#structure.vectors(spin_id='@N', attached='H2', ave=False)
#structure.vectors(spin_id='@N', attached='H5', ave=False)
structure.vectors(spin_id='@N')
#structure.vectors('H',spin_id='@N')
structure.vectors(attached='H', spin_id='@N', ave=False , verbosity=1, unit=False)
# Load spins
#structure.load_spins(spin_id='@N', combine_models=False, ave_pos=False)
# Set the spin name and then load the NH vectors.
#spin.name(spin_id='@N', name='N')
#structure.vectors(spin_id='@N', attached='H', ave=False )
# Load the relaxation data.
relax_data.read(ri_id='R1_600', ri_type='R1', frq=600.03*1e6, file='r1.600.out', mol_name_col=None, res_num_col=1, res_name_col=2, spin_num_col=None, spin_name_col=None, data_col=3,
error_col=4)
relax_data.read(ri_id='R2_600', ri_type='R2', frq=600.03*1e6, file='r2.600.out', mol_name_col=None, res_num_col=1, res_name_col=2, spin_num_col=None, spin_name_col=None, data_col=3, error_col=4)
relax_data.read(ri_id='NOE_600', ri_type='NOE', frq=600.03*1e6, file='noe.600.out', mol_name_col=None, res_num_col=1, res_name_col=2, spin_num_col=None, spin_name_col=None, data_col=3, error_col=4)
relax_data.read(ri_id='R1_700', ri_type='R1', frq=700.13*1e6, file='r1.700.out', mol_name_col=None, res_num_col=1, res_name_col=2, spin_num_col=None, spin_name_col=None, data_col=3, error_col=4)
relax_data.read(ri_id='R2_700', ri_type='R2', frq=700.13*1e6, file='r2.700.out', mol_name_col=None, res_num_col=1, res_name_col=2, spin_num_col=None, spin_name_col=None, data_col=3, error_col=4)
relax_data.read(ri_id='NOE_700', ri_type='NOE', frq=700.13*1e6, file='noe.700.out', mol_name_col=None,
res_num_col=1, res_name_col=2, spin_num_col=None, spin_name_col=None, data_col=3, error_col=4)
# Deselect spins to be excluded (including unresolved and specifically excluded spins).
deselect.read(file='unresolved', dir=None, spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=2, spin_num_col=None, spin_name_col=None, sep=None, spin_id=None, boolean='AND', change_all=False)
deselect.read(file='exclude', spin_id_col=None)
# Set the bond length, CSA values, heteronucleus type, and proton type.
value.set(1.02 * 1e-10, 'r')
value.set(-172 * 1e-6, 'csa')
value.set('15N', 'heteronuc_type')
value.set('1H', 'proton_type')
# Execution.
############
# Do not change!
dAuvergne_protocol(pipe_name=name, diff_model=DIFF_MODEL, mf_models=MF_MODELS, local_tm_models=LOCAL_TM_MODELS, grid_inc=GRID_INC, min_algor=MIN_ALGOR, mc_sim_num=MC_NUM, conv_loop=CONV_LOOP)
----------------------------------------------------------------------------------------------------
relax> pipe.create(pipe_name='mf (Fri May 25 12:23:11 2012)', pipe_type='mf')
relax> sequence.read(file='noe.600.out', dir=None, spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=2, spin_num_col=None, spin_name_col=None, sep=None, spin_id=None)
Opening the file 'noe.600.out' for reading.
relax> spin.name(spin_id=None, name='N', force=False)
relax> structure.read_pdb(file='rS2.pdb', dir=None, read_mol=None, set_mol_name=None, read_model=None, set_model_num=None, parser='internal')
Internal relax PDB parser.
Opening the file 'rS2.pdb' for reading.
Adding molecule 'rS2_mol1' to model None (from the original molecule number 1 of model None)
Adding molecule 'rS2_mol2' to model None (from the original molecule number 2 of model None)
relax>
structure.vectors(attached='H', spin_id='@N', model=None, verbosity=1, ave=True, unit=True)
Extracting vectors from the single model.
Calculating the unit vectors.
The attached atom is a proton.
Extracted N-H vectors for ':1@N'.
Extracted N-H vectors for ':2@N'.
Extracted N-H vectors for ':6@N'.
Extracted N-H vectors for ':7@N'.
Extracted N-H vectors for ':8@N'.
Extracted N-H vectors for ':9@N'.
Extracted N-H vectors for ':10@N'.
Extracted N-H vectors for ':11@N'.
Extracted N-H vectors for ':12@N'.
Extracted N-H vectors for ':13@N'.
Extracted N-H vectors for ':14@N'.
Extracted N-H vectors for ':15@N'.
Extracted N-H vectors for ':16@N'.
Extracted N-H vectors for ':18@N'.
Extracted N-H vectors for ':19@N'.
Extracted N-H vectors for ':20@N'.
Extracted N-H vectors for ':21@N'.
Extracted N-H vectors for ':22@N'.
Extracted N-H vectors for ':23@N'.
Extracted N-H vectors for
':25@N'.
Extracted N-H vectors for ':26@N'.
Extracted N-H vectors for ':27@N'.
Extracted N-H vectors for ':28@N'.
Extracted N-H vectors for ':30@N'.
Extracted N-H vectors for ':31@N'.
Extracted N-H vectors for ':32@N'.
Extracted N-H vectors for ':33@N'.
Extracted N-H vectors for ':34@N'.
Extracted N-H vectors for ':35@N'.
Extracted N-H vectors for ':36@N'.
Extracted N-H vectors for ':38@N'.
Extracted N-H vectors for ':39@N'.
Extracted N-H vectors for ':40@N'.
Extracted N-H vectors for ':41@N'.
Extracted N-H vectors for ':42@N'.
Extracted N-H vectors for ':43@N'.
Extracted N-H vectors for ':44@N'.
Extracted N-H vectors for ':45@N'.
Extracted N-H vectors for ':46@N'.
Extracted N-H vectors for ':47@N'.
Extracted N-H vectors for ':48@N'.
Extracted N-H vectors for ':49@N'.
Extracted N-H vectors for ':50@N'.
Extracted N-H vectors for ':51@N'.
Extracted N-H vectors for
':57@N'.
Extracted N-H vectors for ':58@N'.
Extracted N-H vectors for ':60@N'.
Extracted N-H vectors for ':61@N'.
Extracted N-H vectors for ':62@N'.
Extracted N-H vectors for ':63@N'.
Extracted N-H vectors for ':64@N'.
Extracted N-H vectors for ':65@N'.
Extracted N-H vectors for ':67@N'.
Extracted N-H vectors for ':69@N'.
Extracted N-H vectors for ':70@N'.
Extracted N-H vectors for ':71@N'.
Extracted N-H vectors for ':73@N'.
Extracted N-H vectors for ':74@N'.
Extracted N-H vectors for ':75@N'.
Extracted N-H vectors for ':76@N'.
Extracted N-H vectors for ':77@N'.
Extracted N-H vectors for ':78@N'.
Extracted N-H vectors for ':79@N'.
Extracted N-H vectors for ':80@N'.
Extracted N-H vectors for ':81@N'.
Extracted N-H vectors for ':82@N'.
Extracted N-H vectors for ':83@N'.
Extracted N-H vectors for ':84@N'.
Extracted N-H vectors for ':85@N'.
Extracted N-H vectors for
':86@N'.
Extracted N-H vectors for ':87@N'.
Extracted N-H vectors for ':88@N'.
Extracted N-H vectors for ':89@N'.
Extracted N-H vectors for ':90@N'.
Extracted N-H vectors for ':91@N'.
Extracted N-H vectors for ':92@N'.
Extracted N-H vectors for ':93@N'.
Extracted N-H vectors for ':94@N'.
Extracted N-H vectors for ':98@N'.
Extracted N-H vectors for ':99@N'.
Extracted N-H vectors for ':102@N'.
Extracted N-H vectors for ':103@N'.
Extracted N-H vectors for ':105@N'.
Extracted N-H vectors for ':107@N'.
Extracted N-H vectors for ':108@N'.
Extracted N-H vectors for ':109@N'.
Extracted N-H vectors for ':110@N'.
Extracted N-H vectors for ':111@N'.
Extracted N-H vectors for ':112@N'.
Extracted N-H vectors for ':113@N'.
Extracted N-H vectors for ':114@N'.
Extracted N-H vectors for ':116@N'.
Extracted N-H vectors for ':117@N'.
Extracted N-H vectors for ':118@N'.
Extracted N-H vectors for
':119@N'.
Extracted N-H vectors for ':121@N'.
Extracted N-H vectors for ':123@N'.
Extracted N-H vectors for ':124@N'.
Extracted N-H vectors for ':125@N'.
Extracted N-H vectors for ':126@N'.
Extracted N-H vectors for ':127@N'.
Extracted N-H vectors for ':128@N'.
Extracted N-H vectors for ':129@N'.
Extracted N-H vectors for ':130@N'.
Extracted N-H vectors for ':132@N'.
Extracted N-H vectors for ':133@N'.
Extracted N-H vectors for ':134@N'.
Extracted N-H vectors for ':135@N'.
Extracted N-H vectors for ':136@N'.
Extracted N-H vectors for ':137@N'.
Extracted N-H vectors for ':138@N'.
Extracted N-H vectors for ':139@N'.
Extracted N-H vectors for ':140@N'.
Extracted N-H vectors for ':141@N'.
Extracted N-H vectors for ':142@N'.
Extracted N-H vectors for ':144@N'.
Extracted N-H vectors for ':145@N'.
Extracted N-H vectors for ':146@N'.
Extracted N-H vectors for ':147@N'.
Extracted N-H
vectors for ':148@N'.
Extracted N-H vectors for ':149@N'.
Extracted N-H vectors for ':150@N'.
Extracted N-H vectors for ':152@N'.
Extracted N-H vectors for ':153@N'.
Extracted N-H vectors for ':154@N'.
Extracted N-H vectors for ':155@N'.
Extracted N-H vectors for ':156@N'.
Extracted N-H vectors for ':157@N'.
Extracted N-H vectors for ':158@N'.
Extracted N-H vectors for ':159@N'.
Extracted N-H vectors for ':160@N'.
Extracted N-H vectors for ':161@N'.
relax> structure.vectors(attached='H', spin_id='@N', model=None, verbosity=1, ave=False, unit=False)
Extracting vectors from the single model.
The attached atom is a proton.
RelaxWarning: The bond vector for the spin ':1@N' already exists.
RelaxWarning: The bond vector for the spin ':2@N' already exists.
RelaxWarning: The bond vector for the spin ':6@N' already exists.
RelaxWarning: The bond vector for the spin ':7@N' already
exists.
RelaxWarning: The bond vector for the spin ':8@N' already exists.
RelaxWarning: The bond vector for the spin ':9@N' already exists.
RelaxWarning: The bond vector for the spin ':10@N' already exists.
RelaxWarning: The bond vector for the spin ':11@N' already exists.
RelaxWarning: The bond vector for the spin ':12@N' already exists.
RelaxWarning: The bond vector for the spin ':13@N' already exists.
RelaxWarning: The bond vector for the spin ':14@N' already exists.
RelaxWarning: The bond vector for the spin ':15@N' already exists.
RelaxWarning: The bond vector for the spin ':16@N' already exists.
RelaxWarning: The bond vector for the spin ':18@N' already exists.
RelaxWarning: The bond vector for the spin ':19@N' already exists.
RelaxWarning: The bond vector for the spin ':20@N' already exists.
RelaxWarning: The bond vector for the spin ':21@N' already exists.
RelaxWarning: The bond vector for the spin
':22@N' already exists.
RelaxWarning: The bond vector for the spin ':23@N' already exists.
RelaxWarning: The bond vector for the spin ':25@N' already exists.
RelaxWarning: The bond vector for the spin ':26@N' already exists.
RelaxWarning: The bond vector for the spin ':27@N' already exists.
RelaxWarning: The bond vector for the spin ':28@N' already exists.
RelaxWarning: The bond vector for the spin ':30@N' already exists.
RelaxWarning: The bond vector for the spin ':31@N' already exists.
RelaxWarning: The bond vector for the spin ':32@N' already exists.
RelaxWarning: The bond vector for the spin ':33@N' already exists.
RelaxWarning: The bond vector for the spin ':34@N' already exists.
RelaxWarning: The bond vector for the spin ':35@N' already exists.
RelaxWarning: The bond vector for the spin ':36@N' already exists.
RelaxWarning: The bond vector for the spin ':38@N' already exists.
RelaxWarning: The bond vector
for the spin ':39@N' already exists.
RelaxWarning: The bond vector for the spin ':40@N' already exists.
RelaxWarning: The bond vector for the spin ':41@N' already exists.
RelaxWarning: The bond vector for the spin ':42@N' already exists.
RelaxWarning: The bond vector for the spin ':43@N' already exists.
RelaxWarning: The bond vector for the spin ':44@N' already exists.
RelaxWarning: The bond vector for the spin ':45@N' already exists.
RelaxWarning: The bond vector for the spin ':46@N' already exists.
RelaxWarning: The bond vector for the spin ':47@N' already exists.
RelaxWarning: The bond vector for the spin ':48@N' already exists.
RelaxWarning: The bond vector for the spin ':49@N' already exists.
RelaxWarning: The bond vector for the spin ':50@N' already exists.
RelaxWarning: The bond vector for the spin ':51@N' already exists.
RelaxWarning: The bond vector for the spin ':57@N' already exists.
RelaxWarning: The
bond vector for the spin ':58@N' already exists.
RelaxWarning: The bond vector for the spin ':60@N' already exists.
RelaxWarning: The bond vector for the spin ':61@N' already exists.
RelaxWarning: The bond vector for the spin ':62@N' already exists.
RelaxWarning: The bond vector for the spin ':63@N' already exists.
RelaxWarning: The bond vector for the spin ':64@N' already exists.
RelaxWarning: The bond vector for the spin ':65@N' already exists.
RelaxWarning: The bond vector for the spin ':67@N' already exists.
RelaxWarning: The bond vector for the spin ':69@N' already exists.
RelaxWarning: The bond vector for the spin ':70@N' already exists.
RelaxWarning: The bond vector for the spin ':71@N' already exists.
RelaxWarning: The bond vector for the spin ':73@N' already exists.
RelaxWarning: The bond vector for the spin ':74@N' already exists.
RelaxWarning: The bond vector for the spin ':75@N' already
exists.
RelaxWarning: The bond vector for the spin ':76@N' already exists.
RelaxWarning: The bond vector for the spin ':77@N' already exists.
RelaxWarning: The bond vector for the spin ':78@N' already exists.
RelaxWarning: The bond vector for the spin ':79@N' already exists.
RelaxWarning: The bond vector for the spin ':80@N' already exists.
RelaxWarning: The bond vector for the spin ':81@N' already exists.
RelaxWarning: The bond vector for the spin ':82@N' already exists.
RelaxWarning: The bond vector for the spin ':83@N' already exists.
RelaxWarning: The bond vector for the spin ':84@N' already exists.
RelaxWarning: The bond vector for the spin ':85@N' already exists.
RelaxWarning: The bond vector for the spin ':86@N' already exists.
RelaxWarning: The bond vector for the spin ':87@N' already exists.
RelaxWarning: The bond vector for the spin ':88@N' already exists.
RelaxWarning: The bond vector for the spin
':89@N' already exists.
RelaxWarning: The bond vector for the spin ':90@N' already exists.
RelaxWarning: The bond vector for the spin ':91@N' already exists.
RelaxWarning: The bond vector for the spin ':92@N' already exists.
RelaxWarning: The bond vector for the spin ':93@N' already exists.
RelaxWarning: The bond vector for the spin ':94@N' already exists.
RelaxWarning: The bond vector for the spin ':98@N' already exists.
RelaxWarning: The bond vector for the spin ':99@N' already exists.
RelaxWarning: The bond vector for the spin ':102@N' already exists.
RelaxWarning: The bond vector for the spin ':103@N' already exists.
RelaxWarning: The bond vector for the spin ':105@N' already exists.
RelaxWarning: The bond vector for the spin ':107@N' already exists.
RelaxWarning: The bond vector for the spin ':108@N' already exists.
RelaxWarning: The bond vector for the spin ':109@N' already exists.
RelaxWarning: The bond
vector for the spin ':110@N' already exists.
RelaxWarning: The bond vector for the spin ':111@N' already exists.
RelaxWarning: The bond vector for the spin ':112@N' already exists.
RelaxWarning: The bond vector for the spin ':113@N' already exists.
RelaxWarning: The bond vector for the spin ':114@N' already exists.
RelaxWarning: The bond vector for the spin ':116@N' already exists.
RelaxWarning: The bond vector for the spin ':117@N' already exists.
RelaxWarning: The bond vector for the spin ':118@N' already exists.
RelaxWarning: The bond vector for the spin ':119@N' already exists.
RelaxWarning: The bond vector for the spin ':121@N' already exists.
RelaxWarning: The bond vector for the spin ':123@N' already exists.
RelaxWarning: The bond vector for the spin ':124@N' already exists.
RelaxWarning: The bond vector for the spin ':125@N' already exists.
RelaxWarning: The bond vector for the spin ':126@N' already
exists.
RelaxWarning: The bond vector for the spin ':127@N' already exists.
RelaxWarning: The bond vector for the spin ':128@N' already exists.
RelaxWarning: The bond vector for the spin ':129@N' already exists.
RelaxWarning: The bond vector for the spin ':130@N' already exists.
RelaxWarning: The bond vector for the spin ':132@N' already exists.
RelaxWarning: The bond vector for the spin ':133@N' already exists.
RelaxWarning: The bond vector for the spin ':134@N' already exists.
RelaxWarning: The bond vector for the spin ':135@N' already exists.
RelaxWarning: The bond vector for the spin ':136@N' already exists.
RelaxWarning: The bond vector for the spin ':137@N' already exists.
RelaxWarning: The bond vector for the spin ':138@N' already exists.
RelaxWarning: The bond vector for the spin ':139@N' already exists.
RelaxWarning: The bond vector for the spin ':140@N' already exists.
RelaxWarning: The bond vector for
the spin ':141@N' already exists.
RelaxWarning: The bond vector for the spin ':142@N' already exists.
RelaxWarning: The bond vector for the spin ':144@N' already exists.
RelaxWarning: The bond vector for the spin ':145@N' already exists.
RelaxWarning: The bond vector for the spin ':146@N' already exists.
RelaxWarning: The bond vector for the spin ':147@N' already exists.
RelaxWarning: The bond vector for the spin ':148@N' already exists.
RelaxWarning: The bond vector for the spin ':149@N' already exists.
RelaxWarning: The bond vector for the spin ':150@N' already exists.
RelaxWarning: The bond vector for the spin ':152@N' already exists.
RelaxWarning: The bond vector for the spin ':153@N' already exists.
RelaxWarning: The bond vector for the spin ':154@N' already exists.
RelaxWarning: The bond vector for the spin ':155@N' already exists.
RelaxWarning: The bond vector for the spin ':156@N' already
exists.
RelaxWarning: The bond vector for the spin ':157@N' already exists.
RelaxWarning: The bond vector for the spin ':158@N' already exists.
RelaxWarning: The bond vector for the spin ':159@N' already exists.
RelaxWarning: The bond vector for the spin ':160@N' already exists.
RelaxWarning: The bond vector for the spin ':161@N' already exists.
RelaxError: No vectors could be extracted.
Regards
Jimmy
my log