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
;-)