------ Forwarded Message
From: Mario Garcia <>
Date: Fri, 21 Mar 2003 16:53:17 +0100 (CET)
To:
Subject: Modeller6v2 trouble
Dear Dr. Bozidar,
I have some error after a modeling jot execution (mod script.top) in
Modeller6v2 under an IRIX 6.2 box. Bellow, I include the corresponding
.top and .ali input files and the resulting .log file. Could you give some
hints to help me? Thank you very much in advance for your help.
Regards,
Mario Garcia.
-------------------------------------------------------------------------
Mario Garcia de Lacoba, PhD. Phone : +341 915611800 (ext.4334)
Fax : +341 915627518
Centro de Investigaciones Biologicas E-mail :
C.S.I.C.
c/ Velazquez, 144
28006-Madrid. SPAIN.
-------------------------------------------------------------------------
======================MOB3.top===================================
# Homology modelling by the MODELLER TOP routine 'model'.
INCLUDE # Include the predefined TOP routines
SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file
SET ALNFILE = 'MOB4.ali' # alignment filename
SET KNOWNS = '1cii' # codes of the templates
SET SEQUENCE = '1mob' # code of the target
SET ATOM_FILES_DIRECTORY = './:../atom_files' # 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)
CHECK_ALIGNMENT
CALL ROUTINE = 'model' # do homology modelling
================MOB4.ali================================
C; mob_1cii.phy align
>P1;1cii
structureX:1cii
EIMAVDIYVNPPRVDVFHGTPPAWSSFGNKTIWGGNEWVDDSPTRSDIEK
RDKEITAYKNTLSAQQKENENKRTEAGKRLSAAIAAREKDENTLKTLRAG
NADAADITRQEFRLLQAELREYGFRTEIAGYDALRLHTESRMLFADADSL
RISPREARSLIEQAEKRQKDAQNADKKAADMLAEYERRKGILDTRLSELE
KNGGAALAVLDAQQARLLGQQTRNDRAISEARNKLSSVTESLNTARNALT
RAEQQLTQQKNTPDGKTIVSPEKFPGRSSTNDSIVVSGDPRFAGTIKITT
SAVIDNRANLNYLLSHSGLDYKRNILNDRNPVVTEDVEGDKKIYNAEVAE
WDKLRQRLLDARNKITSAESAVNSARNNLSARTNEQKHANDALNALLKEK
ENIRNQLSGINQKIAEEKRKQDELKATKDAINFTTEFLKSVSEKYGAKAE
QLAREMAGQAKGKKIRNVE-EALKTYEKYRADINKKINAKDRAAIAAALE
SVKLSDISSNLNRFSRGLGYAGKFTSLADWITEFGKAVRTENWRPLFVKT
ETIIAGNAATALVALVFSILTGSALGIIGYGLLMAVTGALIDESLVEKAN
KFW*
>P1;1mob
sequence:1mob
------MSYMVARMQKMKAGNLGGAFKHNERVFETHSNKDINPSRSHLN-
--YELTDRDRSVSYEKQIKDYVNENKVSNRAIRKDAVLCDEWIITSDKD-
-----------FFEKLDEEQTRTFFETAKNYFAENYG-ESNIAYASVHLD
ESTPHMHMGVVPFENGKLSSKAMFDREELKHIQEDLPR--YMSDHGFELE
-------------------------------RGKLNSEAKHKTVAEFKRA
MADMELKEELLEKYHAPLFVDERTG--ELNNDTEAFWHEKEFADMFEVQS
PIRETTNQEKMDWLRKQYQEELKKLESSKKP-LEDDLSHLEELLDKKTKE
YIKIDSEASERASELSKAEGYINTLEN--HSKSLEAKIECLESDNLQLEK
Q----KATKLEAKALNES----ELRELKPKKNFLGKEHYELSPEQ---FE
GLKAEVYRSRTLLHHKDIELEQAKRQVSLRASKNYFTASLERAKEKAKGE
SIDR--LKSEIKRLKN------------E----N-SILRQQNDK-MLGKL
RELMPDKAFKNLLSELKAIKP-----------IVNIIKKAIEKSLF----
---*
=====================MOB4.log=================================
MODELLER 6v2, 17 Feb 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, IRIX64 akilonia 6.5 IP30
Date and time of compilation : 07/05/2002 17:12:26
Job starting time (YY/MM/DD HH:MM:SS): 2003/03/21 23:47:53.033
TOP_________> 105 705 SET ALNFILE = 'MOB4.ali'
TOP_________> 106 706 SET KNOWNS = '1cii'
TOP_________> 107 707 SET SEQUENCE = '1mob'
TOP_________> 108 708 SET ATOM_FILES_DIRECTORY = './:../atom_files'
TOP_________> 109 709 SET STARTING_MODEL = 1
TOP_________> 110 710 SET ENDING_MODEL = 1
TOP_________> 111 711 CHECK_ALIGNMENT
check_a_343_> >> BEGINNING OF COMMAND
check_a_335E> No alignment.
recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Dynamically allocated memory at finish [B,kB,MB]: 2200483
2148.909 2.099
Starting time : 2003/03/21
23:47:53.033
Closing time : 2003/03/21
23:48:02.202
Total CPU time [seconds] : 0.00
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