Dear MODELLER users,

I installed modeller onto my computer. It looks as though I am having problems getting the program to run properly.

I am running the program using bash instead of csh. In the installation, I accepted all defaults except for the program location. The program is located in a directory named /modeller. The program then can be found in /modeller/bin/mod6v2.

Running the tutorial files included in the installation seem to work. I think that model-default.top is working properly. The problem comes when I attempt to run the tutorials from http://salilab.org/modeller/user_manual.shtml.

The first tutorial generates this message:

$ mod6v2 seq_search.top /modeller/bin/mod6v2: line 38: 1360 Killed $NICE ${EXECUTABLE} $STEERF >$LOGF

The seq_search.top file looks like this:

SET SEARCH_RANDOMIZATIONS = 100 SEQUENCE_SEARCH FILE = 'TvLDH.ali', ALIGN_CODES = 'TvLDH', DATA_FILE =ON

I read that going into emacs and saving it may clear up the problem, but it did not.

The output file seq_search.log starts off well I think. But I don' t know if the end is correct. It aligns over 800 sequences. From the .top file, I thought it would only align 100 sequences.

Here is the start:

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, Linux dhcppc2 2.4.18-14 i686 Date and time of compilation : 07/16/2002 11:42:16 Job starting time (YY/MM/DD HH:MM:SS): 2003/07/28 22:20:50.755

seqsearc_> 1 TvLDH 1xnb 335 185 63 18.81 34.05 117083.50

_aln.pos 10 20 30 40 50 60 TvLDH MSEAAHVLITGAAGQIGYILSHWI-ASGELYGDRQVYLHLLDIPPAMNRLTALTMELEDCAFPHLAGF 1xnb ASTDYWQNWT-DGG--G-IVNA-VNGSG---GN---Y----SV----N-WSN-T-G--N--F--VVG- _consrvd * * * * * ** * * * * * *

_aln.p 70 80 90 100 110 120 130 TvLDH VATTDPKAAFKDIDCAFLVASMPLKPGQVRADLISSNSVIFKNTGEYLSKWAKPSVKVLVIGNPDNTN 1xnb ------KG-WT----T---GS-PF-----RT--I--N---Y-NAG--V--WA-PN------GN-GY-- _consrvd * * * * * * * * ** * **

_aln.pos 140 150 160 170 180 190 200 TvLDH CEIAMLHAKNLKPENFSSLSMLDQNRAYYEVASKLGVDVKDVHDIIVWGNHGESMVADLTQATFTKEG 1xnb --LT-LYGWT-R----SPL--IE----YY-V-----VD--S------WGTY--R--P--T-GTY-K-G _consrvd * * * ** * ** ** * * * *

_aln.pos 210 220 230 240 250 260 270 TvLDH KTQKVVDVLDHDYVFDTFFKKIGHRAWDILEHRGFTSAASPTKAAIQHMKAWLFGTAPGEVLSMGIPV 1xnb -TVKS-DGGTYD-IYTT--TRYN--APSI-D--G--DR-T-T-FT-QY---W---SV-RQ--S-K--R _consrvd * * * * * * * * * * * *

_aln.pos 280 290 300 310 320 330 TvLDH PEGNPYGIKPGVVFSFPCNVDKEGKIHVVEGFKV-NDWLREKLDFTEKDLFHEKEIALNHLAQGG 1xnb PTGSN-A-T--ITFT-N-HVNA-WKSH---GMNLGSNWAYQVMA-TE-G-YQSSG-SSN-VTVW- _consrvd * * * * * * * * ** *

It continues on until this point.

_aln.pos 280 290 300 310 320 330 TvLDH EGNPYGIKPGVVFSFPCNVDKEGKIHVVEGFKVNDWLREKLDFTEKDLFHEKEIALNHLAQGG 1ayaA Q---Y-------Y-----M--E-H-H---G-Q----LKEK-N--G-DVI-ELKYPLN------ _consrvd * * * * * ** * * **

seqsearc_> 897 TvLDH 1az4A 335 187 77 22.99 41.18 123537.50

_aln.pos 10 20 30 40 50 60 TvLDH MSEAAHVLITGAAGQI-GYILSHWIASGELYGDRQVYLHLLDIPPAMNRLTALTMELEDCAFPHLAGF 1az4A -SLRSD-LIN-ALYDVCG-IIS---A--E--G-K-IY------P-----LSTI-FEL----FS-RP-I _consrvd * ** * * * * * * * * * * ** *

(Fundamental)--L32747--Bot-----------------

This leads me to think that it went over its 100 alignment limit and ended up timing out. I'm not sure how many hours this took. I believe it was over four hours. As you can see, the output file is 32 747 lines long.

Here is what the install program included with the .bashrc file. I've removed the key in case you don't want it displayed in the forum.

### begin MODELLER6v2##################################################

MODINSTALL6v2=/modeller EXECUTABLE_TYPE6v2=i386-absoft LIBS_LIB6v2=$MODINSTALL6v2/modlib/libs.lib KEY_MODELLER6v2=xxx mod=mod6v2 export MODINSTALL6v2 EXECUTABLE_TYPE6v2 LIBS_LIB6v2 KEY_MODELLER6v2 mod PATH=$PATH:$MODINSTALL6v2/bin ulimit -S -s unlimited

### end MODELLER6v2####################################################

My computer has a 500 mb swap file. I don't know if that is adequate or if it is not enough for this program. Perhaps I am missing another setting of some sort.

Your help would be much appreciated. I've been trying to get the program to work for over a week so I'm perplexed.

Thanks

Andrew L University of Idaho ;-)