Hi,
I have just installed Modeller 6.0v1 on my P-III, Conectiva Linux (RH-like), under /usr/local/bin/modeller6v1/
My .bashrc reads:
# .bashrc # User specific aliases and functions # Source global definitions if [ -f /etc/bashrc ]; then . /etc/bashrc fi ### begin MODELLER6v1 ######################################################
MODINSTALL6v1=/usr/local/bin/modeller6v1 EXECUTABLE_TYPE6v1=i386-absoft LIBS_LIB6v1=$MODINSTALL6v1/modlib/libs.lib KEY_MODELLER6v1=XXX mod=mod6v1 export MODINSTALL6v1 EXECUTABLE_TYPE6v1 LIBS_LIB6v1 KEY_MODELLER6v1 mod PATH=$PATH:$MODINSTALL6v1/bin ulimit -S -s unlimited
### end MODELLER6v1 ########################################################
Attempts to run Modeller:
1. When I try 'mod model-default'I get 'bash: mod: command not found'
2. When I try '/usr/local/bin/modeller6v1/bin/mod6v1 model-default'I get 'STOP'
3. When I try '/usr/local/bin/modeller6v1/bin/mod6v1_i386-absoft model-default' I get something more interesting:
MODELLER 6v1, 17 Jan 2002
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2002 Andrej Sali All Rights Reserved
Written by A. Sali with help from A. Fiser, R. Sanchez, M.A. Marti-Renom, B. Jerkovic, A. Badretdinov, F. Melo, J.P. Overington & E. Feyfant Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux home.localdomain 2.2.17-14cl i686 Date and time of compilation : 01/24/2002 16:28:15 Job starting time (YY/MM/DD HH:MM:SS): 2002/02/27 16:50:50.084
fullfn__230E> File not found: model-default Directories: :${MODINSTALL6v1}/bin/ Extensions : .top: Prefixes : nothing, pdb recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Dynamically allocated memory at finish [B,kB,MB]: 2190959 2139.608 2.089 Starting time : 2002/02/27 16:50:50.084 Closing time : 2002/02/27 16:50:51.154 Total CPU time [seconds] : 1.03 STOP
I trust someone can help me.
Yours thankfully,
Ari M. Siqueira, PhD Associate Professor of Biochemistry ICB - UFMG Brazil
Hi,
It looks like you don't have the top file you are trying to execute in the same dir from which you are invoking mod6v1. Installation looks OK, since executable runs, but you need to specify .top file as an input for the MODELLER.
Please refer to the manual for more details. Just don't give up. It's very frustrating at the beginning. Feel free to ask any questions you might have.
Happy modeling, Bozidar
-----Original Message----- From: owner-modeller_usage@salilab.org [mailto:owner-modeller_usage@salilab.org] On Behalf Of Ari M. Siqueira Sent: Wednesday, February 27, 2002 3:09 PM To: modeller_usage@salilab.org Subject: starting modeller: what's wrong?
Hi,
I have just installed Modeller 6.0v1 on my P-III, Conectiva Linux (RH-like), under /usr/local/bin/modeller6v1/
My .bashrc reads:
# .bashrc # User specific aliases and functions # Source global definitions if [ -f /etc/bashrc ]; then . /etc/bashrc fi ### begin MODELLER6v1 ######################################################
MODINSTALL6v1=/usr/local/bin/modeller6v1 EXECUTABLE_TYPE6v1=i386-absoft LIBS_LIB6v1=$MODINSTALL6v1/modlib/libs.lib KEY_MODELLER6v1=XXX mod=mod6v1 export MODINSTALL6v1 EXECUTABLE_TYPE6v1 LIBS_LIB6v1 KEY_MODELLER6v1 mod PATH=$PATH:$MODINSTALL6v1/bin ulimit -S -s unlimited
### end MODELLER6v1 ########################################################
Attempts to run Modeller:
1. When I try 'mod model-default'I get 'bash: mod: command not found'
2. When I try '/usr/local/bin/modeller6v1/bin/mod6v1 model-default'I get 'STOP'
3. When I try '/usr/local/bin/modeller6v1/bin/mod6v1_i386-absoft model-default' I get something more interesting:
MODELLER 6v1, 17 Jan 2002
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2002 Andrej Sali All Rights Reserved
Written by A. Sali with help from A. Fiser, R. Sanchez, M.A. Marti-Renom, B. Jerkovic, A. Badretdinov, F. Melo, J.P. Overington & E. Feyfant Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux home.localdomain 2.2.17-14cl i686 Date and time of compilation : 01/24/2002 16:28:15 Job starting time (YY/MM/DD HH:MM:SS): 2002/02/27 16:50:50.084
fullfn__230E> File not found: model-default Directories: :${MODINSTALL6v1}/bin/ Extensions : .top: Prefixes : nothing, pdb recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Dynamically allocated memory at finish [B,kB,MB]: 2190959 2139.608 2.089 Starting time : 2002/02/27 16:50:50.084 Closing time : 2002/02/27 16:50:51.154 Total CPU time [seconds] : 1.03 STOP
I trust someone can help me.
Yours thankfully,
Ari M. Siqueira, PhD Associate Professor of Biochemistry ICB - UFMG Brazil
I had a similar problem running on a linux box.
>1. When I try 'mod model-default'I get 'bash: mod: command not found' I have the same error. Try just 'mod6v1 topfile'.
>2. When I try '/usr/local/bin/modeller6v1/bin/mod6v1 model-default'I get >'STOP' This worked check your log file 'model-default.log' I have been running it by 'mod6v1 topfile' and it seems to work fine.
>3. When I try '/usr/local/bin/modeller6v1/bin/mod6v1_i386-absoft >model-default'
Make sure 'model-defualt' is in the local directory that your running it from.
I hope this helped.
Michael Buck
************************************************ Michael Buck NCSU Genetics mjbuck@unity.ncsu.edu Phone (919)515-5759 Fax (919)515-3355 http://www4.ncsu.edu/~mjbuck *************************************************
participants (3)
-
Ari M. Siqueira -
Bozidar -
Michael Buck