March 2005 - modeller_usage

TYROSINE KINASE HOMOLOGY MODELLING
by Obdulia Rabal 29 Mar '05

29 Mar '05

Dear modellers, Could anybody advise to me a standard / traditional manner of dealing with domain tyrosine kinase insert (KID) when homology modelling tyrosine kinases? I have looked for some literature but only a pair of references remark this point. Thanks in advance Obdulia

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dear modeller
by arul prakasam 27 Mar '05

27 Mar '05

dear modeller iam modeling a model which has hetero atom FE in it active site the FE is present in my template and in my target.so in order to model my model with hetero atom what should i do. sir in library of atom residue(i.e .,in modlib/restyb.lib) as FE is not found what should i give pdb three and one letter code and CHARMM code. is this process is correct thanking in regards Yahoo! India Matrimony: Find your life partneronline.

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Problem with modeller7v7
by Magali Cottevieille 25 Mar '05

25 Mar '05

Dear Sir, I need your help about a problem I encounter with modeller 7v7 : I have the following error message : Array too small. Increase MANGPF I can't find where I can modify the value of MANGPF !!! Maybe it will be helpful for you to know that I have modified parameter and topology files to add the definitions of a Fe4S4 cluster. Thanks a lot for your help. Best regards, Magali Cottevieille. --------------------------------------------------------------------------------- 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, Linux lagaffe.lmcp.jussieu.fr 2.6.10-1.770_FC2 i686 Date and time of compilation : 09/14/2004 11:06:39 Job starting time (YY/MM/DD HH:MM:SS): 2005/03/25 14:53:53.585 rdparf__223E> Array too small. Increase MANGPF current maximum, current need: 600 601 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 77847 76.022 0.074 Starting time : 2005/03/25 14:53:53.585 Closing time : 2005/03/25 14:53:55.735 Total CPU time [seconds] : 1.09 -- Magali COTTEVIEILLE Laboratoire de Minéralogie Cristallographie Paris, Campus BOUCICAUT case 115, 140 Rue de Lourmel 75015 Paris, France. Tel: +33 (0)1 44 27 52 41 Fax: +33 (0)1 44 27 37 85 E-mail : magali.cottevieille(a)lmcp.jussieu.fr URL : http://www.lmcp.jussieu.fr/~cottevie/

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NOC (current version 1.5.2.10) a new, free program for protein structure model-building, visualization, validation and analysis ...
by Chenmengen 24 Mar '05

24 Mar '05

http://noc.ibp.ac.cn/ Highlights of NOC: Easy-to-use; Novel and precise structures representation; Auto-fit residues' side-chain against density data; Solid surface calculation, generation and electrostatic potential, hydrophobic force coloring; Easy to superimpose structures; Structure validation; Hardware 3D-Stereo Visualizing Support; Molecular animate model generation; Potentials calculation; Analyze the trajectory of Amber;

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dear modeller
by arul prakasam 23 Mar '05

23 Mar '05

dear modeller iam modeling a model which has hetero atom FE in it active site the FE is present in my template and in my target.so in order to model my model with hetero atom what should i do. sir in library of atom residue(i.e .,in modlib/restyb.lib) as FE is not found what should i give pdb three and one letter code and CHARMM code. is this process is correct thanking in regards Yahoo! India Matrimony: Find your life partneronline.

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Problems modelling sections of sequence on different templates
by pitm0020＠flinders.edu.au 20 Mar '05

20 Mar '05

Hi all, I am trying to model my protein on two templates except in a small region in the middle of my sequence which I want to model on a third template only. I have altered the .ali files so that there are gaps in the correct parts of the alignments and changed the pdb files to have corresponding gaps. When I run this it comes up with an error and doesn't make a _fit file: fit2xyz_296E> Number of equivalent positions < 3: 0 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 If I don't model this small piece and leave the gaps in the other templates it works fine so this suggests that there is something wrong with the third template or how I assigned it but I cannot figure it out. Any help would be greatly appreciated as I have a deadline approaching! Thanks! Below are the .ali and .top files >P1;1XFD structureX:1XFD:127:A:849:A:::: ------------------------------------------------------------ ---------------------QKKKVTVEDLFSEDFKIHDPEAKWISDTEFIYREQKGTV RLWNVETNTSTVLIEGKKIESLRAIR--YEISPDREYALFSYNVEPIYQHSYTGYYVLSK IPHGDPQSLDPPEVSNAKLQYAGWGPKG-QQLIFIFENNIYYCAHVGKQAIRVVSTG--- ---KEGVIYNGLSDWLYEEEILKTHIAHWWS------PDG-------------------- -----------------------PSISLHVIGLN--------GPTHDLEMMPPDDPRMRE YYITMVKWATSTKVAV-TWLNRAQNVSILTLCDATTGVCTKKHEDESEAWLHRQN----- -------------------EEPVFSKDGRKFFFIRAIPQGGRGKFYHITVS--------- -----SSQPNSSNDNIQSITSGDWDVTK----ILAYDEKGNKIYFLSTEDLPRRRQLYSA NTVGNFNRQCLSCDLVEN-CTYFSASFSHSMDFFLLKCEGPGVPMVTVHNTTDKKKMFDL ETNEHVKKAINDR--QMPKVEYRDIEIDDYNLPMQILKPATFTDTTHYPLLLVVDGTPGS QSVAEKFE--VSWETVMVSSHGAVVVKCDGRGSGFQGTKLLHEVRRRLGLLEEKDQMEAV RTML-KEQYIDRTRVAVFGKDYGGYLSTYILPAKGENQGQTFTCGSALSPITDFKLYASA FSERYLGLHGLDN--RAYEMTKVAHRVSALEEQQFLIIHPTADEKIHFQHTAELITQLIR GKANYSLQIYPDESHYFTSSSLKQHLYRSIINFFVECFRI----------------* >P1;1H2W structureX:1H2W:208:A:250:A:::: ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ----------------------------------------QKLYYHVLGTDQSEDILCAE FPDEPKWMGGAELSDDGRYVLLS------------------------------------- ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ ------------------------------------------------------------ --------------------------------------------------------* >P1;1N1M structureX:1N1M:39:A:764:A:::: ------------------------------------------------------------ ---------------------SRKTYTLTDYLKNTYRLKLYSLRWISDHEYLYKQENN-I LVFNAEYGNSSVFLENSTFDEFGHSINDYSISPDGQFILLEYNYVKQWRHSYTASYDIYD LN---KRQLITEERIPNNTQWVTWSPVG-HKLAYVWNNDIYVKIEPNLPSYRITWTG--- ---KEDIIYNGITDWVYEEEVFSAYSALWWS------PNG-------------------- -----------------------PTVKFFVVNTDSLSS---VTNATSIQITAPASMLIGD HYLCDVTWATQERISL-QWLRRIQNYSVMDICDYDESSGRWNCLVARQHIEMSTTGWVG- ---------------RFRPSEPHFTLDGNSFYKIISNEEGYRHICYFQID---------- ------------KKDCTFITKGTWEVIG----IEALTSDYLYYISNEYKGMPGGRNLYKI QLSDYTKVTCLSCELNPERCQYYSVSFSKEAKYYQLRCSGPGLPLYTLHSSVNDKGLRVL EDNSALDKMLQNV--QMPSKKLDFIILNETKFWYQMILPPHFDKSKKYPLLLDVYAGPCS QKADTVFR--LNWATYLASTENIIVASFDGRGSGYQGDKIMHAINRRLGTFEVEDQIEAA RQFS-KMGFVDNKRIAIWGWSYGGYVTSMVLG----SGSGVFKCGIAVAPVSRWEYYDSV YTERYMGLPTPEDNLDHYRNSTVMSRAENFKQVEYLLIHGTADDNVHFQQSAQISKALVD VGVDFQAMWYTDEDHGIASSTAHQHIYTHMSHFIKQCFS-----------------* >P1;DP8mod sequence:DP8mod:.:.:.:.:::: MAAAMETEQLGVEIFETADCEENIESQDRPKLEPFYVERYSWSQLKKLLADTRKYHGYMM AKAPHDFMFVKRNDPDGPHSDRIYYLAMSGENRENTLFYSEIPKTINRAAVLMLSWKPLL DLFQATLDYGMYSREEELLRERKRIGTVGIASYDYHQGSGTFLFQAGSGIYHVKDGGPQG FTQQPLRPNLVETSCPNIRMDPKLCPADPDWIAFIHSNDIWISNIVTREERRLTYVHNEL ANMEEDARSAGVATFVLQEEFDR-YSGYWWCPKAETTPSGGKILRILYEENDESEVEIIH VTSPMLETRRADSFRYPKTGTANPKVTFKMSEIMIDAEGRIIDVIDKELIQPFEILFEGV EYIARAGWTPEGKYAWSILLDRSQTRLQIVLISPELFIPVEDDVMERQRLIESVPDSVTP LIIYEETTDIWINIHDIFHVFPQSHEEEIEFIFASECKTGFRHLYKITSILKESKYKRSS GGLPAPSDFKCPIKEEIAITSGEWEVLGRHGSNIQVDEVRRLVYFEGTKDSPLEHHLYVV SYVNPGEVTRLTDRGYSHSCCISQHCDFFISKYSNQKNP-HCVSLYKLSSPEDDPTCKTK EFWATILDSAGPLPDYTPPEIFSFESTTGFTLYGMLYKPHDLQPGKKYPTVLFIYGGPQV QLVNNRFKGVKYFRLNTLASLGYVVVVIDNRGSCHRGLKFEGAFKYKMGQIEIDDQVEGL QYLASRYDFIDLDRVGIHGWSYGGYLSLMALMQ----RSDIFRVAIAGAPVTLWIFYDTG YTERYMGHPDQNEQGYYLGSVAMQAEKFPSEPNRLLLLHGFLDENVHFAHTSILLSFLVR AGKPYDLQIYPQERHSIRVPESGEHYELHLLHYLQENLGSRIAALKVI--------* INCLUDE # Include the predefined TOP routines SET ALNFILE = 'C:\Program Files\Modeller7v7\Models\DP8mod.ali' # Alignment filename SET KNOWNS = '1XFD' '1H2W' '1N1M' # Code of the template SET SEQUENCE = 'DP8mod' SET STARTING_MODEL = 1 SET ENDING_MODEL = 1 SET DEVIATION = 4.0 # Amount of randomization between models SET LIBRARY_SCHEDULE = 1 # thorough VTF schedule SET MAX_VAR_ITERATIONS = 300 SET FINAL_MALIGN3D = 1 # MALIGN3D and write superposed # templates & models SET MD_LEVEL = 'refine_1' # thorough MD annealing CALL ROUTINE = 'model'

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regarding Interaction Energy...
by Himanshu Grover 20 Mar '05

20 Mar '05

Hi, I am trying to model a protein complex, with 2 chains. I wish to know the interaction energy between the two chains at the end of model-generation. Is it possible to do this, taking into account both, van-der-waal's interactions as well as coulombic? Is the energy value, that appears at the top of each generated model pdb file, indicative of the same (While optimizing the structure, I have Dynamic Lennard and Dynamic Coulomb switches on, and others off.) I am not looking for the internal energy of the whole protein complex, but just the interaction energy of the 2 comprising chains. Any help would be appreciated. Thanks and regards, Himanshu Grover

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work help
by randy garmon 18 Mar '05

18 Mar '05

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help
by arul prakasam 18 Mar '05

18 Mar '05

hai dear modeller while running the modeller i got the error below can u suggest me how to rectify thanking you 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, Linux hcl4 2.4.20-8 i686 Date and time of compilation : 09/12/2004 21:24:59 Job starting time (YY/MM/DD HH:MM:SS): 2005/03/18 16:25:06.597 TOP_________> 109 749 SET ALNFILE = 'alignment.ali' TOP_________> 110 750 SET KNOWNS = 'pdb1lox' TOP_________> 111 751 SET SEQUENCE = 'HUMAN' TOP_________> 112 752 SET STARTING_MODEL = 1 TOP_________> 113 753 SET ENDING_MODEL = 1 TOP_________> 114 754 CALL ROUTINE = 'model' TOP_________> 115 419 CALL ROUTINE = 'getnames' TOP_________> 116 534 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATI ON; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL' TOP_________> 117 535 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERA TI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; ' TOP_________> 118 536 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE TOP_________> 119 537 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE TOP_________> 120 538 SET ROOT_NAME = SEQUENCE TOP_________> 121 539 RETURN TOP_________> 122 420 CALL ROUTINE = 'homcsr' TOP_________> 123 112 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQ UE; NCE Dynamically allocated memory at amaxseq [B,kB,MB]: 84067 82. 097 0.080 openf5__224_> Open 20 OLD SEQUENTIAL alignment.ali openf5__224_> Open 13 OLD SEQUENTIAL ./pdb1lox.pdb Dynamically allocated memory at amaxbnd [B,kB,MB]: 10758819 10506. 659 10.260 openf5__224_> Open 20 OLD SEQUENTIAL alignment.ali openf5__224_> Open 13 OLD SEQUENTIAL ./pdb1lox.pdb rdpir___648E> Alignment sequence not found in PDB file: 1 ./pdb1lox.pdb recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 10758819 10506. 659 10.260 Starting time : 2005/03/18 16:25:06. 597 Closing time : 2005/03/18 16:25:07. 194 Total CPU time [seconds] : 0.59 ________________________________________________________________________ Yahoo! India Matrimony: Find your life partner online Go to: http://yahoo.shaadi.com/india-matrimony

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Allocate error 494-reg
by Elavazhagan 17 Mar '05

17 Mar '05

Hello wisdoms, When I give command as mod7v7 align2d.top to predict the alignment file ,I have got error as (Allocate error 494: Allocation of Array with extent of 8008900 failed End of diagnostics ) in the command line,but in the log file I got neither warning nor error. How can I rectify this probleem? Thanks in advance. -- E.Elavazhagan 09444332083

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