January 2005 - modeller_usage

(no subject)
by Johnwin Silvester 23 Jan '05

23 Jan '05

Cen Gao wrote: " Hi, I am new to modeller,Now I am just doing some simple test on a protein,but both the target and template has some atom file other than residue which i have to consider during the simulation.So i have to include the HETATM_IO = 'on' in simulation,my top file is as follow:" Hi, the problem may be here the template sequence count and the pdb sequence count is not same. In most pdb structures, we could find an amino acid missing at the begining. Verify whether the first template sequence aa is same with first aa in pdb sequence(spdbv control panel). probably you can get some other template of if theres no good alignment for that first amino acid, simply remove it. May this work regards, johnwin

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doubt regarding modller usage
by E rajakumar 22 Jan '05

22 Jan '05

Sir I have installed modeller7v7 in windows2000. The input files are in 'C:/Program Files/Modeller7v7 after running the mod7v7 model-default, it could recognise model-default.top file but log file is showing that alignment file is not found please, could u mail me what is the problem? thank you in advance. rajkumar The log file is as follows 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, Win2000 build 2195 Service Pack 2, E007A, uni, x86 Family 15 Model 2 Stepping 4 Date and time of compilation : 09/13/2004 17:17:22 Job starting time (YY/MM/DD HH:MM:SS): 2005/01/22 20:25:10.812 TOP_________> 109 749 SET ALNFILE = 'c:/Program Files/Modeller7v7/alignment' TOP_________> 110 750 SET KNOWNS = '1amu' TOP_________> 111 751 SET SEQUENCE = '1fax' TOP_________> 112 752 SET ATOM_FILES_DIRECTORY = 'c:/Program Files/Modeller7v7/; 1amu' TOP_________> 113 753 SET STARTING_MODEL = 1 TOP_________> 114 754 SET ENDING_MODEL = 1 TOP_________> 115 755 CALL ROUTINE = 'model' TOP_________> 116 419 CALL ROUTINE = 'getnames' TOP_________> 117 534 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL' TOP_________> 118 535 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; ' TOP_________> 119 536 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE TOP_________> 120 537 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE TOP_________> 121 538 SET ROOT_NAME = SEQUENCE TOP_________> 122 539 RETURN TOP_________> 123 420 CALL ROUTINE = 'homcsr' TOP_________> 124 112 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE Dynamically allocated memory at amaxseq [B,kB,MB]: 84067 82.097 0.080 fullfn__230E> File not found: c:/Program Files/Modeller7v7/alignment Directories: Extensions : :.ali Prefixes : nothing, pdb recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 84067 82.097 0.080 Starting time : 2005/01/22 20:25:10.812 Closing time : 2005/01/22 20:25:12.140 Total CPU time [seconds] : 1.19 ________________________________________________________________________ Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now http://uk.messenger.yahoo.com/download/index.html

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Question on an error message
by Cen Gao 22 Jan '05

22 Jan '05

Hi, I am new to modeller,Now I am just doing some simple test on a protein,but both the target and template has some atom file other than residue which i have to consider during the simulation.So i have to include the HETATM_IO = 'on' in simulation,my top file is as follow: INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 SET ALNFILE = 'seq.ali' SET KNOWNS = '1U19' SET SEQUENCE = '1U20' SET TOPOLOGY_MODEL = 1, HETATM_IO = 'on', WATER_IO = 'on' SET TOPLIB = '$(LIB)/top.lib' SET PARLIB = '$(LIB)/par.lib' SET STARTING_MODEL = 1 SET ENDING_MODEL = 1 CALL ROUTINE = 'model' But it give me some error information rdabrk__290E> Number of residues in the alignment and pdb files are different: 696 697 For alignment entry: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 I don't why,because the alignment file and pdb file is exactly right(I simply generate the alignment file from the pdb file using modeller). And if I don't turn HETATM_IO = 'on' and simply using the code INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 SET ALNFILE = 'seq.ali' SET KNOWNS = '1U19' SET SEQUENCE = '1U20' SET STARTING_MODEL = 1 SET ENDING_MODEL = 1 CALL ROUTINE = 'model' It works very well and give me the right target file.I am really confused about that.Can anyone give me some suggestion about my code.And I also wanna to ask if i want to take the non-residue atoms into consideration during modeller,is my method right?Thank you for your suggestion.

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Modeller multiple alignment
by Andreas Kowarsch 21 Jan '05

21 Jan '05

Hello all, i also tried to run my skript to create a multiple alignment. top-file: READ_MODEL FILE = '1HYZ.pdb', MODEL_SEGMENT 'FIRST:A''LAST:A' SEQUENCE_TO_ALI ALIGN_CODES = '1HYZ' READ_MODEL FILE = '1BIS.pdb', MODEL_SEGMENT 'FIRST:B''LAST:B' SEQUENCE_TO_ALI ALIGN_CODES = '1BIS',ADD_SEQUENCE = on READ_MODEL FILE = '1BIU.pdb', MODEL_SEGMENT 'FIRST:B''LAST:B' SEQUENCE_TO_ALI ALIGN_CODES = '1BIU',ADD_SEQUENCE = on SET ATOM_FILES = '1HYZ' '1BIS' '1BIU' MALIGN3D SET ADD_SEQUENCE = on, ALIGN_BLOCK = NUMB_OF_SEQUENCES READ_ALIGNMENT FILE = 'target.ali', ALIGN_CODES = ALIGN_CODES 'target', ADD_SEQUENCE = on ALIGN2D WRITE_ALIGNMENT FILE='target.ali', ALIGNMENT_FORMAT = 'PIR' WRITE_ALIGNMENT FILE='target.pap', ALIGNMENT_FORMAT = 'PAP' But my job don't terminate.... it always made the same log file log-file: Job starting time (YY/MM/DD HH:MM:SS): 2005/01/13 14:15:56.678 rdactio_534E> Command not recognized: recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 56755 55.425 0.054 Starting time : 2005/01/14 14:15:56.678 Closing time : 2005/01/14 14:15:57.612 Total CPU time [seconds] : 0.90 Please can anybody help me....

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Modeller 7v7 Stack problems, tried EVERYTHING!!!!
by Tom Petty 21 Jan '05

21 Jan '05

I have a windows XP SP2 IBM laptop with plenty of memory (512MB RAM) and processing speed. When I try to model a protein domain of about 750 residues (with a multiple alignment of only two sequences, the target and the strucutre sequence), the program runs for about 20-30 seconds and then I get this error: C:\Program Files\Modeller7v7\examples\tutorial-model>mod7v7 Toms-Initial forrtl: severe (170): Program Exception - stack overflow Image PC Routine Line Source mod7v7.exe 00507271 Unknown Unknown Unknown mod7v7.exe 004FEA3E Unknown Unknown Unknown mod7v7.exe 004589DE Unknown Unknown Unknown mod7v7.exe 0040653E Unknown Unknown Unknown mod7v7.exe 0040F5BB Unknown Unknown Unknown mod7v7.exe 006A564B Unknown Unknown Unknown mod7v7.exe 006EDB39 Unknown Unknown Unknown mod7v7.exe 006DC824 Unknown Unknown Unknown kernel32.dll 7C816D4F Unknown Unknown Unknown I've done all that is in my power to bump the memory management on my laptop, changing the virtual memory and paging sizes (to max). Editing the CONFIG.NT to explicitly stating number of stacks and stack size, etc. Nothing works! It seems that my computer should be able to handle modeller, no? Would you have any suggestions as to what may be going on and how to handle this? Also, I worked through the tutorial and it runs fine with the example files. Thanks for your help, All the best Tom Petty ----------------------------------- Graduate Student Genomics and Computational Biology Biomedical Graduate Studies University of Pennsylvania

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question
by drugdesign 18 Jan '05

18 Jan '05

I want to make homology modelling of TM domains without loops in GPCR. But I get error during calculatioons. What wrong I have done? Respectively yours, Andrew I use such alignment: >P1;1L9H X-ray:1L9H:37 : :307 : :rhodopsin:Bos Taurus: : FSMLAAYMFLLIMLGFPINF/YILLNLAVADLFMVFGGFTTT/NLEGFFATLGGEIALWSLVVL/AIMGVAFTWVMALACAAPPLV/FVIYMFVVHFIIPLIVIFFC/VTRMVIIMVIAFLICWLPYAG/FMTIPAFFAKTSAVYNPVIYI* >P1;1fdx sequence:fzd1:324 : :623 : :Frizzled:Homo Sapiens: : GIWSVLCCASTLFTVLTYLV/IIFLSGCYTAVAVAYIAGFLL/TILFMMLYFFSMASSIWWVIL/YFHLAAWAVPAIKTITILALG/FVLAPLFVYLFIGTSFLLAGF/IGVFSVLYTVPATIVIACYFY/VFMIKYLMTLIVGITSGFWIW *

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RE: [modeller_usage] question
by Schweikardt, Thorsten 18 Jan '05

18 Jan '05

Hi Andrew, it's hard to say what goes wrong as your email does not contain the error message or your input files, but I would guess the line X-ray:1L9H:37 : :307 : :rhodopsin:Bos Taurus: : causes the problem, it should read like this: structureX:1L9H:37 : :307 : :rhodopsin:Bos Taurus: : You should consult the modeller manual about the correct input file formats, to make sure there is not anything else wrong with your alignment: http://salilab.org/modeller/manual/node64.html I hope that helps. Best wishes, Thorsten Schweikardt Molekulare Biophysik Universität Mainz

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Re: modeller_usage Digest, Vol 4, Issue 1
by rathan kar 13 Jan '05

13 Jan '05

hi all iam facing a problem and i dont know as to which software should i use: 1. i have a protein whose first 100 residues matches one domain and the rest 136 residues a second one. is it logical to join these two domains and construct a protein and say that this protein has dual function. 2. if yes, then how do the orgins of these two models coincide. as far as i know we should use a rotation matrix to align these two. but i need a readymade software which is user freindly so that this can do that work. are there any such softwares other than INSIGHTII. PLZ REPLY --------------------------------- Do you Yahoo!? The all-new My Yahoo! Get yours free!

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