- modeller_usage - salilab.org

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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Re: modeller_usage Digest, Vol 4, Issue 21
by drugdesign 17 Mar '05

17 Mar '05

You can use Autodock program. It's a free software for docking studies. All the best! Andrew >Hi! All: >I need do some docking studies. It would be greatly appreciated if anyone can recommend some good free softwares. >Thanks a lot Tong Tong Chen School of Biological Sciences Flinders University GPO Box 2100 Adelaide 5001 Email: Tong.Chen(a)flinders.edu.au Phone: (08) 8201-3836

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USING OF RESTRAIN FILE 'RSR' FOR OPTIMISATION OF MODEL
by apurba kumar samal 16 Mar '05

16 Mar '05

Respected Sir, Myself Apurba Kumar Samal, student of indian institute of information technology Allahabad. Sir I am doing my project on structure of Falcipain-3, a cystiene protease from PLASMODIUM FALCIPARUM.I am using your software for modelling,MODELLER7v7. When i verify the structure by verification server it shows deviation in bone length. For rectification i tried to use bond restrain. It gives the x.rsr files. I could not understand how can I use that file to rectify my model. How can I use that file to rectify my model. what are the command i have to use this file on my predicted structure.Sir my work has now stopped for that please sir help me how to move further. Waiting for your positive and early response. Thanking you. Apurba Kumar Samal. M.Tech. Bioinformatics, IIIT-A asamal_bi03(a)iiita.ac.in

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how can i apply 'rsr' file for optimisation of my model
by apurba kumar samal 16 Mar '05

16 Mar '05

Respected Sir, Myself Apurba Kumar Samal, student of indian institute of information technology Allahabad. Sir I am doing my project on structure of Falcipain-3, a cystiene protease from PLASMODIUM FALCIPARUM.I am using your software for modelling,MODELLER7v7. When i verify the structure by verification server it shows deviation in bone length. For rectification i tried to use bond restrain. It gives the x.rsr files. I could not understand how can I use that file to rectify my model. How can I use that file to rectify my model. what are the command i have to use this file on my predicted structure.Sir my work has now stopped for that please sir help me how to move further. Waiting for your positive and early response. Thanking you. Apurba Kumar Samal. M.Tech. Bioinformatics, IIIT-A asamal_bi03(a)iiita.ac.in

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version 6 and 7 scripts
by Paula R.=?ISO-8859-1?Q?_Kuser_Falc=E3o?= 16 Mar '05

16 Mar '05

Dear Modeller I was using the script Align2D.top below to run modeller with version 6.2. Now that we installed version 7, I just can't get it to work. I get the following message: read_al_375E> Unknown residue type,position,sequence: 1 2 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Could you please let me know what is wrong? Thanks, Paula Kuser Align2D.top ############################################# # ALIGNING OUR TARGET WITH THE TEMPLATE # # file.pdb - your template pdb file # pdb name - template code # seq.txt - target file in pir format # seq - target code # file.ali - constructed alignment file ############################################# # Include MODELLER library scripts #INCLUDE # Defining our local pdb directory for input #SET ATOM_FILES_DIRECTORY = '/db/pdb' # Reading template pdb file READ_MODEL FILE = '1ig8.pdb' # Defining code of the template SEQUENCE_TO_ALI ALIGN_CODES = '1ig8' # Reading our target READ_ALIGNMENT FILE = 'seq.txt', ALIGN_CODES = ALIGN_CODES 'HEX', ADD_SEQUENCE = on # Alignment ALIGN2D # Alignment in pir formate WRITE_ALIGNMENT FILE='HEXTC.ali', ALIGNMENT_FORMAT = 'PIR' Here is the seq.txt file: ######################################################### # #TARGET SEQUECE IN PIR FORMAT # ########################################### >P1;HEX sequence:HEX:.:.:.:. MSARLNNLLQHIAVKDKDSDTMRHLKQRMALASLANQFTVGKDHLKQLMLYMVHQMIEG LEGRESTLRMLPSYVYKTDPSKATGVFYALDLGGTNFRVLRVTCKEGRVADRVDAKFVI PQQALQGTAEDLFGFIAQSVKKMMEQKAPEDLNRTVPLGFTFSFPTEQKGVDHGFLIKW TKGFSTRGVEGKDVVELLQKALKRMEVKVKVVALCNDTVGTLITNYFFDPDTQVGVIIG TGSNACYFEDAYAVTKEPSVAARGTTQTPINMECGNFDSKYKFVLPVTAYDEAMDAVTP NRNFQTQEKMVSGMYLGEISRRMIAHLAELHCLPSALASKMAKPWSFETKFMGMISADR MPGLQFTRQVFQELFQVDVTDVADLHVIRDVCCLVRGRAAQISAMFCSAPLVKTRKEGR ATVAIDGSVFEKTPSFRRLLQQNMNAILGPGCDVTTALARDGSGIGAAFISALVVNDK* Paula Kuser Falcão Laboratório de Bioinformática Estrutural Embrapa Informática Agropecuária -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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Thanks to our groups for quick response
by rajesh rengaraj 15 Mar '05

15 Mar '05

Dear friends, Thanks for sharing your valuable time with me and your quick response for my queries. You brought me out from the darkness. Thank you. Yahoo! India Matrimony: Find your life partneronline.

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