- modeller_usage - salilab.org

Help on align.top
by Liu Shiyong 06 Jul '04

06 Jul '04

Dear all, I just did a modelling based on a model(1L9H). My align2d.top is : protein:~/syliu>more align2d.top INCLUDE READ_MODEL FILE = '1L9H' SEQUENCE_TO_ALI ALIGN_CODES = '1L9H' READ_ALIGNMENT FILE = 'tget.ali', ALIGN_CODES = ALIGN_CODES 'tget', ADD_SEQUENCE = on ALIGN2D WRITE_ALIGNMENT FILE='tget-1L9H.ali', ALIGNMENT_FORMAT = 'PIR' WRITE_ALIGNMENT FILE='tget-1L9H.pap', ALIGNMENT_FORMAT = 'PAP' My target sequence is : protein:~/syliu>more tget.ali >P1;tget sequence:tget:::::::0.00: 0.00 MNTSAPPAVSPNITVLAPGKGPWQVAFIGITTGLLSLATVTGNLLVLISFKVNTELKTVNNYFLLSLACADLIIGTFSMNLYTTYLLMGHWALGTLACDLWLAL DYVASNASVMNLLLISFDRYFSVTRPLSYRAKRTPRRAALMIGLAWLVSFVLWAPAILFWQYLVGERTVLAGQCYIQFLSQPIITFGTAMAAFYLPVTVMCTLY WRIYRETENRARELAALQGSETPGKGGGSSSSSERSQPGAEGSPETPPGRCCRCCRAPRLLQAYSWKEEEEEDEGSMESLTSSEGEEPGSEVVIKMPMVDPEAQ APTKQPPRSSPNTVKRPTKKGRDRAGKGQKPRGKEQLAKRKTFSLVKEKKAARTLSAILLAFILTWTPYNIMVLVSTFCKDCVPETLWELGYWLCYVNSTINPM CYALCNKAFRDTFRLLLLCRWDKRRWRKIPKRPGSVHRTPSRQC* When I do mod align2d.top , the modeller ends successfully and output a "STOP". But I got a log: MODELLER 6v2, 17 Feb 2002 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2002 Andrej Sali All Rights Reserved Written by A. Sali with help from A. Fiser, R. Sanchez, M.A. Marti-Renom, B. Jerkovic, A. Badretdinov, F. Melo, J.P. Overington & E. Feyfant 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 protein 2.4.18-14 i686 Date and time of compilation : 07/16/2002 11:42:16 Job starting time (YY/MM/DD HH:MM:SS): 2004/07/06 23:22:21.841 dispers_247E> Internal error: 641 642 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 25421225 24825.414 24.244 Starting time : 2004/07/06 23:22:21.841 Closing time : 2004/07/06 23:37:12.289 Total CPU time [seconds] : 832.85 So, what is the problem on the error information ? (dispers_247E> Internal error: 641 642)? Shiyong Liu

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Special distance restraints weighting
by Schweikardt, Thorsten 06 Jul '04

06 Jul '04

Hello everyone, I would like to know if there is a possibility to force Modeller to use a certain distance in a model, even if that means distorting the template by a great value? I am using user distance restraints as shown in Modeller's manual. I am trying to build a model of a protein where the distance between two loops is 20 Angstroms bigger than in the template - problem is, the models would not adopt the given distance, but would stick more or less to the conformation of the template structure as the sequence identity is very high. I presume this high sequence identity results in a strong contribution to the molecular pdf, and this prevents the loops to modelled in the requested conformation. Does anyone know how to solve this problem? Thorsten Schweikardt Molecular Biophysics University of Mainz

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problem with structures
by Marcin Hus 04 Jul '04

04 Jul '04

Dear Sir, We are starting work with Modeller on the base of "Comparative protein structure modeling with Modeller: A practical approach". We have a problem with work of the script 'compare.top'. We obtained the following message: pntdp___252E> increase MAXRES or gap penalties. recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 When we removed 'MALIGN3D' command from the script it seems to work but execution of the next script 'align2d.top' looked as follows: Dynamically allocated memory at amaxseq [B,kB,MB]: 2200483 2148. 909 2.099 TOP_________> 2 2 READ_MODEL FILE = '1f88.pdb' openf5__224_> Open 11 OLD SEQUENTIAL 1f88.pdb Dynamically allocated memory at amaxbnd [B,kB,MB]: 12194587 11908. 776 11.630 openf5__224_> Open 11 OLD SEQUENTIAL 1f88.pdb rdatm___297_> Segments, residues, atoms: 2 643 5069 rdatm___298_> Segment: 1 1 A 1 A 2639 rdatm___298_> Segment: 2 1 B 1 B 2430 iatmcls_286W> MODEL atom not classified: ALA:OT1 ALA iatmcls_286W> MODEL atom not classified: ALA:OT2 ALA iatmcls_286W> MODEL atom not classified: ASN:OT1 ASN TOP_________> 3 3 SEQUENCE_TO_ALI ALIGN_CODES = '1f88A' TOP_________> 4 4 READ_ALIGNMENT FILE = 'korhum.ali', ALIGN_CODES = 'korh um; ', ADD_SEQUENCE = ON openf5__224_> Open 11 OLD SEQUENTIAL korhum.ali Dynamically allocated memory at amaxbnd [B,kB,MB]: 12227463 11940. 882 11.661 openf5__224_> Open 11 OLD SEQUENTIAL korhum.ali read_al_374_> Non-standard residue type,position,sequence: / 339 1 read_al_374_> Non-standard residue type,position,sequence: / 645 1 Read the alignment from file : korhum.ali Total number of alignment positions: 645 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 korhum 643 3 1f88A undefined TOP_________> 5 5 ALIGN2D Dynamically allocated memory at amaxbnd [B,kB,MB]: 24499233 23925. 031 23.364 align2d_276_> ALIGN_BLOCK changed to 1. pdbnam__217W> Filename for PDB code not found: 1f88A Directories: ./ Extensions : :.atm:.pdb:.ent:.crd rdabrk__288W> Protein not accepted: 1 mkapsa__293W> No TOPOLOGY_LIB is in memory. Use READ_TOPOLOGY to read one. openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib//as1.sim.m at rdrrwgh_268_> Number of residue types: 20 dispers_247E> Internal error: 642 643 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 24499233 23925. 031 23.364 Starting time : 2004/06/21 10:13:11. 753 Closing time : 2004/06/21 10:13:15. 768 Total CPU time [seconds] : 3.92 Please suggest what we did wrong. Thank You. Marcin Hus Medical University in Lublin Poland

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2quest.: howto add restraints & rand_seed
by Sascha Tayefeh 04 Jul '04

04 Jul '04

Dear community, having searched the whole of the manual as well as past posts, I could find helpful contributions, so I'm trying to find help here. I'm facing to questions: 1. RESTRAINTS: I didn't get the idea of how to *ADD* restraints to those modeller makes itself. Actually, I didn't get the idea of how manually add restraints with modeller, at all (remark: I'm a Charmm-User). So here is what I want to do, maybe some could help me with a little script: I'd like to fix the coordinates of all atoms of a slice of residues (e.g. Res 10-23). All the rest of the restraints are supposed to be calculated by modeller. 2. RAND_SEED: Is there a way to define the random seed for the "CALL ROUTINE = 'model'" command? Thank you very much in advance -- S.Tayefeh

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Problem with PDB file
by Lucas Bleicher 30 Jun '04

30 Jun '04

Dear colleagues, I�m facing a problem with Modeller6, and although it seems to be a common one (I�ve seen similar requests in the list archives), I just couldn�t fix it reading the previous posts nor the FAQ. The PDB file I�m using as a template starts at residue 8 and ends at residue 315. So, my alignement is as follows: ======================================================= C; A sample alignment in the PIR format; used in tutorial >P1;1DKU structureX:1DKU:8 : :315 : :PRPP:bacilo: 1.90: 0.19 NLKIFSLNSNPELAKEIADIVGVQLGKCSVTRFSDGEVQINIEESIRGCDCYIIQSTSDPVNEHIMELLIMVDALKRASAKTINIVIPYYGY ARQDRKARSREPITAKLFANLLETAGATRVIALDLHAPQIQGFFDIPIDHLMGVPILGEYFEGKNLE--DIVIVSPDHGGVTRARKLADRLKAPIAIIDK RRPRPNVAEVMNIVGNIEGKTAILIDDIIDTAGTITLAANALVENGAKEVYACCTHPVLSGPAVERINNSTIKELVVTNSIKLPEEKK-IERFKQLSVGP LLAEAIIRVHEQQSVSYLFS----* >P1;HUMA sequence:HUMA:8 : :315 : :PRPP:Homo sapiens: 2.00:-1.00 NIKIFSGSSHQDLSQKIADRLGLELGKVVTKKFSNQETCVEIGESVRGEDVYIVQSGCGEINDNLMELLIMINACKIASASRVTAVIPCFPY ARQDKKDKSRAPISAKLVANMLSVAGADHIITMDLHASQIQGFFDIPVDNLYAEPAVLKWIRENISEWRNCTIVSPDAGGAKRVTSIADRLNVDFALIHK ERKKANEVDRMVLVGDVKDRVAILVDDMADTCGTICHAADKLLSAGATRVYAILTHGIFSGPAISRINNACFEAVVVTNTIPQEDKMKHCSKIQVIDISM ILAEAIRRTHNGESVSYLFSHVPL* ======================================================= The .top file was directly edited from the example model-default.top, and is as follows: ====================================================== # Homology modelling by the MODELLER TOP routine 'model'. INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 2 # uncomment to produce a large log file SET ALNFILE = 'ALIN.pir' # alignment filename SET KNOWNS = '1DKU' # codes of the templates SET SEQUENCE = 'HUMA' # code of the target SET ATOM_FILES_DIRECTORY = '/mod6v2/examples/tutorial-model/' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate) CALL ROUTINE = 'model' # do homology modelling ===================================================== Both the alignement file "ALIN.pir" and PDB file "1DKU.pdb" are on the /mod6v2/examples/tutorial-model/ directory. But although the program actually opens this pdb file, it shows this message: rdabrk__288W> Protein not accepted: 1 rdabrk__290E> Number of residues in the alignment and pdb files are different: 309 0 For alignment entry: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Does anybody has any hint on how to fix this problem? Thanks in advance, Lucas Bleicher __________________________________ Do you Yahoo!? Read only the mail you want - Yahoo! Mail SpamGuard. http://promotions.yahoo.com/new_mail

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Re: [modeller_usage] optimization problem...
by Eric Feyfant 30 Jun '04

30 Jun '04

Hi; Yes you can do it. I you are sure about the interaction sites and the orientation, I will suggest you to build manually the complex and use the resulting model as template and build a new model. But this time use the "strongest" optimization routine (see the manual it is routine 3 or 1 I don't remember". Also depend on the result you may have to eliminate some restraint that may bias the final model. I hope it helps. Eric ------------------------------------ Eric Feyfant, Ph.D. Senior research Scientist Computational Chemistry Wyeth Research 200 Cambridge Park Drive Cambridge, MA 02140 tel: +1 617 665 5656 fax: +1 617 665 5682 email: efeyfant(a)wyeth.com >>> "Himanshu Grover" <hgrover_00(a)iiita.ac.in> 6/30/2004 8:04:44 AM >>> hi, being a new user, I am facing many problems with modeller. now consider a situation in which i want to model only one particular domain/protein in a protein-protein complex, since the structure for the other domain/protein is available, but then i want to optimize the binding region of the modelled domain taking into context, the other domain as well... is it possible that i use the optimization routine of modeller for the same, only after putting both the proteins of the complex into proper interacting/binding orientation, so that energy minimization can be performed taking into context the entire complex and not just the modelled part thanks, for helping out... sincerely. _______________________________________________ modeller_usage mailing list modeller_usage(a)salilab.org http://salilab.org/mailman/listinfo/modeller_usage

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optimization problem...
by Himanshu Grover 30 Jun '04

30 Jun '04

hi, being a new user, I am facing many problems with modeller. now consider a situation in which i want to model only one particular domain/protein in a protein-protein complex, since the structure for the other domain/protein is available, but then i want to optimize the binding region of the modelled domain taking into context, the other domain as well... is it possible that i use the optimization routine of modeller for the same, only after putting both the proteins of the complex into proper interacting/binding orientation, so that energy minimization can be performed taking into context the entire complex and not just the modelled part thanks, for helping out... sincerely.

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modelling proteins with multiple chains...
by Himanshu Grover 28 Jun '04

28 Jun '04

hi, i need some help with modelling a protein comprised of multiple chains. Firstly, is it possible to model the entire protein in one go, or diff. chains need to be modelled separately... Secondly, I want to provide my own alignment with the template, and am not using modeller's alignment routine... if I have to model 2 chains of the protein together, how do I provide the alignment... as the chains might not be contiguous... Moreover, when I do so, the resultant structure of modeller sticks together the loose ends of the 2 chains, as if they were continuous strands. This affects the model at the ends of the chains...How do I tell that this is the first chain and that is the second?? thanks, your sincerely, himan

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Two templates
by Han Choe 25 Jun '04

25 Jun '04

Dear all, I'm trying to model a protein structure using two homologous proteins as templates. I wonder how much the two known structures should be close for the modeling because I get errors like the following, stdevs__397E> STDEV < 0: -0.3487 Set to 1E-5. When I used the two known structures separately one by one, the modeling worked fine. Cheers, Han

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too slow...
by noha lim 24 Jun '04

24 Jun '04

Dear all, I just started using modeller a few weeks ago. And now I'm doing an example(seq_search.top) in the website. But it takes so long time(about 3 hours). And I think that's right, because in the seq_search.log file from website it also took 2 hours. Then why is it so slow? Others(like BLAST or something) take only a few seconds to find sequences. What are the big differences?? Thank you!! Noha Lim _________________________________________________________________ FREE pop-up blocking with the new MSN Toolbar get it now! http://toolbar.msn.click-url.com/go/onm00200415ave/direct/01/

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