Dear all Modeller user,
I follow by so near this question and answers because I have the same error message.
I do the download of "Updated Windows binary" and I have the same problem of STACK OVERFLOW.
I do my example (top scripts) exactly as the example from Modeller basic tutorial avec my data, of course.
My sequence file is :
>P1;rpb3 sequence:rpb3:::::::0.00: 0.00 MVALTVEELTPEHIRFTLSNTTVGYANALRRILISEVPTIAIDMVEIERNNTVLPDEVLA HRLGLIPIYSKRELKYKEECSCSGFCSECSVVFEIDVVHTDDTLRTVSTRDIVCDEEDVI IKSGPVITKLARDQGLKARCIGRKGVGKTHAKWSPVSAISFEYDKDNVRRETNYWFEESI EEEWPGVRQGEANLMQKIDKIHMCVEVVEGGAGPLAVVLEGLRILKEKVATLSSAAETMD *
My script file is:
# Example to ALIGN RPB3 with the Template # # the template is 1i50C (pdb1i50.ent at C:\Program Files\Modeller7v7\examples\Testes\atom_files) # SET OUTPUT_CONTROL = 1 1 1 1 0
# directory with input atom files SET ATOM_FILES_DIRECTORY = './:../atom_files'
READ_MODEL FILE = 'pdb1i50.ent'
SEQUENCE_TO_ALI ALIGN_CODES = ALIGN_CODES '1i50C', ATOM_FILES=ALIGN_CODES , ADD_SEQUENCE = on
READ_ALIGNMENT FILE = 'rpb3.ali', ALIGN_CODES = ALIGN_CODES 'rpb3'
ALIGN2D
WRITE_ALIGNMENT FILE='rpb3-1i50.ali', ALIGNMENT_FORMAT = 'PIR' WRITE_ALIGNMENT FILE='rpb3-1i50.pap', ALIGNMENT_FORMAT = 'PAP'
I find an information at the FAQ messages that there are a Modeller's Variable called "MAXRES". I follow this suggestion from an modeller user: SET MAXRES=5000, and I did not get sucessful!!! but if I uses this ligne above:
SET MAXRES = 50000000
I have no 'stack overflow' error message but I have '_E> modeller error message (se the log file above)
Can you give some help ?
Many thanks.
My LOG file is :
MODELLER 7v7, Sep 12, 2004 09:15pm
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2004 Andrej Sali All Rights Reserved
Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom, N. Eswar, F. Alber, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA 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, WinXP build 2600 Service Pack 2, SANTOS, uni, x86 Family 15 Model 2 Stepping 9 Date and time of compilation : 09/13/2004 17:17:22 Job starting time (YY/MM/DD HH:MM:SS): 2005/01/24 12:06:44.218
TOP_________> 2 2 SET ATOM_FILES_DIRECTORY = './:../atom_files'
TOP_________> 3 3 READ_MODEL FILE = 'pdb1i50.ent'
openf5__224_> Open 11 OLD SEQUENTIAL ../atom_files\pdb1i50.ent openf5__224_> Open 11 OLD SEQUENTIAL ../atom_files\pdb1i50.ent rdatm___297_> Segments, residues, atoms: 10 3558 28279 rdatm___298_> Segment: 1 2 A 1450 A 11154 rdatm___298_> Segment: 2 18 B 1224 B 8711 rdatm___298_> Segment: 3 3 C 268 C 2095 rdatm___298_> Segment: 4 1 E 215 E 1760 rdatm___298_> Segment: 5 72 F 155 F 679 rdatm___298_> Segment: 6 2 H 146 H 1068 rdatm___298_> Segment: 7 1 I 122 I 997 rdatm___298_> Segment: 8 1 J 65 J 532 rdatm___298_> Segment: 9 1 K 114 K 919 rdatm___298_> Segment: 10 25 L 70 L 364 TOP_________> 4 4 SEQUENCE_TO_ALI ALIGN_CODES = ALIGN_CODES '1i50C', ATOM_F; ILES =ALIGN_CODES , ADD_SEQUENCE = ON
TOP_________> 5 5 SET MAXRES = 50000000
TOP_________> 6 6 READ_ALIGNMENT FILE = 'rpb3.ali', ALIGN_CODES = ALIGN_COD; ES 'rpb3'
openf5__224_> Open 20 OLD SEQUENTIAL rpb3.ali amaxres_215E> Dynamic memory allocation failed. Routine, variable, status: irestypn2 2 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Dynamically allocated memory at finish [B,kB,MB]: 2102291815 2053019.375 2004.902 Starting time : 2005/01/24 12:06:44.218 Closing time : 2005/01/24 12:08:38.125 Total CPU time [seconds] : 37.66
> Tom Petty wrote: > > I have a windows XP SP2 IBM laptop with plenty of memory (512MB > RAM) .... > >C:\Program Files\Modeller7v7\examples\tutorial-model>mod7v7 Toms-Initial >forrtl: severe (170): Program Exception - stack overflow > > > > This means that Modeller has exceeded the stack space limit. This a > constant, set when the Modeller binary was linked, so it won't help if > you add more memory to your machine. > ... > > Alternatively, you can download just such a 'fixed' binary from the > Modeller downloads page: > http://salilab.org/modeller/download_installation.html > (The link is right at the bottom: "Updated Windows binary".) > Use this binary to replace the existing mod7v7.exe file in your > Modeller installation (by default it should be in > C:\Program Files\modeller7v7\bin), and all should be well. > >If these problems persist, let me know. > > > Ben Webb, Modeller Caretaker >