July 2004 - modeller_usage

beta strand restriction
by John Simms 14 Jul '04

14 Jul '04

Hi All, Sorry for the two emails but i forgot to ask something. Has anyone managed to resolve the beta strand restraining. I have seen that several groups have had a problem, but i cant find any solutions. Anyone had any luck?? Cheers John

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loop modelling with secondary structure
by John Simms 14 Jul '04

14 Jul '04

Hi All, Has anyone tried, or is it possible, to model large loops using the loop tool under the added constraints of disulphide bonds and/or secondary structure(beta strands)??Any results. Cheers John

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Nucleic Acids and modeller
by Luis Rosales 06 Jul '04

06 Jul '04

Hi! I need to model a protein complexed to a nucleic acid... I know my alignment should look like: PROTEIN/NUCLEIC-ACID But I was wondering if I should define new libraries in my top file and how do you tell modeller: "Hey, this is a nucleic acid, A stands for adenine!!" (I will be working with poly Uracil...) Thank you in advance for your help. Best regards, Luis Rosales

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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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