Maybe it is the missing s in
etenv EXECUTABLE_TYPE6v0 iris4d
?
Best, Andrej
--
Andrej Sali, Professor
Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and
California Institute for Quantitative Biomedical Research
Mission Bay Genentech Hall
600 16th Street, Suite N472D
University of California, San Francisco
San Francisco, CA 94143-2240 (CA 94107 for direct delivery by courier)
Tel +1 (415) 514-4227; Fax +1 (415) 514-4231
Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, 4233, 4239
Email ; Web http://salilab.org
> -----Original Message-----
> From:
> [">mailto:] On Behalf Of Modeller Care
> Sent: Friday, March 21, 2003 7:57 AM
> To:
> Subject: FW: Modeller6v2 trouble
>
>
>
> ------ 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
>
>
> ------ End of Forwarded Message
>