[modeller_usage] problems running scripts under mod7v7
To:
Subject: [modeller_usage] problems running scripts under mod7v7
From: Edoardo Saccenti <>
Date: Mon, 31 Jan 2005 11:49:40 +0100
Organization: CERM
I have the following script and alignment files and these
work fine under mod6v2:
TOP FILE:
INCLUDE # Include the predefined TOP routines
SET OUTPUT_CONTROL = 1 1 1 1 1
SET ALNFILE = 'TYMS_G157V.aln' # alignment filename
SET KNOWNS = '1HW3'
SET SEQUENCE = 'TYMS_G157V'
SET HETATM_IO = on
SET HYDROGEN_IO = on
SET ATOM_FILES_DIRECTORY = './' # directories for input atom files
SET STARTING_MODEL= 1 # index of the first model
SET ENDING_MODEL = 1 # index of the last model
# (determines how many models to
calculate)
CALL ROUTINE = 'model' # do homology modelling
ALIGN FILE:
>P1;1HW3
structureX:1HW3:26 :A:310:A :TYMS:Homo Sapiens:-1.00:-1.00
PPHGELQYLGQIQHILR-GVRKDDRTGTGTLSVFGMQARYSLRDEFPLLTTKRVFWKGVL
EELLWFIKGSTNAKELSSKGV----------------------GDLGPVYGFQWRHFGAE
YRDMESDYSGQGVDQLQRVIDTIKTNPDDRRIIM-AWNPRDLPLMALPP-HAL-QFYVVN
SELSCQLYQRSGDMGLGVPFNIASYALLTYMIAHITGLKPGDFIHTLGDAHIYLNHIEPL
KIQLQREPRPFPKLRILRKVEKIDDFKAEDFQIEGYNPHPTIKME
*
>P1;TYMS_G157V
sequence:TYMS_G157V: : : : :::-1.00:-1.00
PPHGELQYLGQIQHILR-GVRKDDRTGTGTLSVFGMQARYSLRDEFPLLTTKRVFWKGVL
EELLWFIKGSTNAKELSSKGVKIWDANGSRDFLDSLGFSTREEGDLGPVYGFQWRHFGAE
YRDMESDYSGQVVDQLQRVIDTIKTNPDDRRIIM-AWNPRDLPLMALPP-HAL-QFYVVN
SELSCQLYQRSGDMGLGVPFNIASYALLTYMIAHITGLKPGDFIHTLGDAHIYLNHIEPL
KIQLQREPRPFPKLRILRKVEKIDDFKAEDFQIEGYNPHPTIKME
*
Running the same files under version mod7v7 the program stops withe following
LOG file:
rdactio_534E> Command not recognized:
recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
There is some differnece between input files for 6 and 7 versions?
Thanks
edoardo
--
"Raffiniert ist der Herr Gott,
aber boshaft ist Er nicht."
---
Dr. Edoardo Saccenti
FiorGen Pharmacogenomics Foundation
CERM Nuclear Magnetic Resonace Research Center
Scientific Pole - University of Florence
Via Luigi Sacconi n° 6
50019 Sesto Fiorentino (FI)
tel: +39 055 4574193
fax: +39 055 4574253
www.cerm.unifi.it