- modeller_usage - salilab.org

Same coordinates
by Joanne Hanna 08 Apr '05

08 Apr '05

Hi I am trying to use modeller to rebuild 5 missing resdiues from a protein that I wish to do some MD on. Whilst I have managed to do this, the x, y and z corrdinates of the modeller output models are all slightly different for each atom for the region of the protein of known structure (i am modelling the sequence against its structure minus the 5 residues). As I was hoping to add to this new complete structure the coordinates of the ligands in the original pdb file, I was wondering if there is any way to define that all the coordinates should be excactly the same as those from the original structure and the only alterations would be the addition of the positions of the 5 'new' residues. Thanks Jo

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question re. Modeller6v2 (re. fold)
by Vicente Reyes 04 Apr '05

04 Apr '05

Dear Dr. Sali & colleagues, I used Modeller6v2 to build 3-D models of some unsolved protein sequences, using as input sequence alignments obtained from the threading program, 123D. Since Modeller performs a partial rfefinement of the structure it builds, do you think it is possible that the fold of the final 3-D structure would be different from the fold of the alignment template found by 123D? Have you seen a case where the fold was altered by the refinement performed by Modeller? How often does this happen and in what particular cases? Thank you very much for your time and your help. Very sincerely yours, V. Reyes ====================================================== >>>>>>>>>>>> VICENTE M. REYES, Ph.D. <<<<<<<<<<<< Dept. of Pharmacol., Sch. of Pharm. & Pharm. Sci., & Integrative Biosci. Dept., S.D. Supercomputer Center Univ. of California-San Diego, La Jolla, CA 92093-0505

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request
by selvaraj manikandan mani 04 Apr '05

04 Apr '05

Respected sir, I have downloaded MODELLER and when I want to use it I could not get the concept like how to get the alignment file and the script file when I went through the manual.I would like to do a modelling of the following sequence: >dmpr MPIKYKPEIQHSDFKDLTNLIHFQSMEGKIWLGEQRMLLLQFSAMASFRREMVNTLG IERAKGLFLRHGYQSGLKDAELARKLRPNASEVGMFLAGPQMHSLKGLVKVRPTELD IDKEYGRFYAEMEWIDSFEVEICQTDLGQMQDPVCWTLLGYACAYSSAFMGREIIFKE VSCRGCGGDKCRVIGKPAEEWDDVASFKQYFKNDPIIEELYELQSQLLSLRTNLDKQE GQYYGIGQTPAYQTVRNMMDKAAQGKVSVLLLGETGVGKEVIARSVHLRSKRAAEPFV AVNCAAIPPDLIESELFGVEKGAFTGATQSRMGRFERADKGTIFLDEVIELSPRAQASL LRVLQEGELERVGDNRTRKIDVRVIAATHEDLAEAVKAGRFRADLYYRLNVFPVAIPAL RERREDIPLLVEHFLQRFHQEYGKRTLGLSDKALEACLHYSWPGNIRELENVIERGIIL TDPNESISVQALFLRAPEEPQTASERVSLDGVLIQPGNGQGSWISQLLSSG LSLDEIEESLMREAMQQANQNVSGAARLLGLSRPALAYRLKKIGIEG and the PDB ID for the templete is 1NY5. Sir,please do help me how can I proceed further.

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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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