- modeller_usage - salilab.org

Re: [Fwd: limit in READ_RESTRAINTS]
by Andras Fiser 25 May '99

25 May '99

Hi Dong, you can deal with your problems (too many pseudoatoms) in two ways: either explicitly defining all the pairs of atoms (or at least a few of them - you defined 291 independent pseudoatom) that you restraining, or using a modeller version suited for this particular problem. Since this morning you can find a modeller executable with 2000 possible pseudo atoms, on our ftp site: ftp salilab.org /pub/outgoing/mod_r10000 Andras -- , Andras Fiser, PhD # phone: (212) 327 7206 The Rockefeller University # fax: (212) 327 7540 Box 270, 1230 York Avenue # e-mail:fisera@rockefeller.edu New York, NY 10021-6399, USA # http://salilab.org/~andras

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Re: [Fwd: limit in READ_RESTRAINTS]
by Andras Fiser 24 May '99

24 May '99

Mensur, The description of the form of restraints is given in the manual setion 2.5 page 73. Dong, we got your modeller files that failed to deal with the nmr restarints. You gave 2 files of restraints with 500 and 1000 input lines and the larger one failed to work with modeller, modeller crashed with memory fault. The same effect was reproduced here, but it happened not because of the larger restraints file. Multiplying the size of the smaller file (beyond 1000 entry lines) worked fine. The real problem is that in total you use more than 200 pseudatom in your larger file (undefined number of restrained Hydrogens is counted as pseudoatom). The number of pseduoatom in your smaller file (in total) is 159, that is while it worked. Modeller 4 uses static arrays, so the array sizes are predefined, as you can see in the header of the log file (and below), the array size of pseudoatoms is 200. mod 5, which will come out soon, uses dynamic memory allocation and you will not have this problem. Best wishes Andras ----------- mod4 default ---------------- Array dimensions (!8/9/96!): Maximum number of residues : 2000 Maximum number of atoms : 32000 Maximum length of alignment : 2000 Maximum number of sequences in alignment : 20 Maximum number of restrained features : 320000 Maximum number of restraint parameters : 3200000 Maximum number of restraint atoms : 960000 Maximum number of non-bonded atom pairs : 180000 Maximum number of non-bonded restraint types : 1 Maximum number of non-bonded restraint type parms: 1 Maximum number of explicitly excluded pairs : 100 Maximum number of pseudo atoms : 200 Maximum optimization schedule length : 50 ----------------------------------------------- -- , Andras Fiser, PhD # phone: (212) 327 7206 The Rockefeller University # fax: (212) 327 7540 Box 270, 1230 York Avenue # e-mail:fisera@rockefeller.edu New York, NY 10021-6399, USA # http://salilab.org/~andras

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Re: limit in READ_RESTRAINTS
by Mensur 24 May '99

24 May '99

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limit in READ_RESTRAINTS
by Dong Xu 21 May '99

21 May '99

Dear Modellers, I am using experimental NOE restraints to improve models in case of weak homology between a target and its template. The NOE restraint file was included as: READ_RESTRAINTS FILE = 'nmr_2igh.rsr' However, when the file contains many entries (>1000 restraints), the following error message occurs: iup2crm_E> IUPAC atom not found in topology library: H act34___E> indpsd(i) out of range; ireal, natm: 0 2953 The MODELLER runs fine when number of NOE entries is smaller than 500, and the output model shows improvement when using NOE restraints. I assume for restraint file with "MODELLER12 VERSION: USER FORMAT" has an upper bound for number of allowed entries. Is there any way that I can get around this problem? Thanks, -Dong Xu http://compbio.ornl.gov/~nxy

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multiple and not overlapping templates
by Andras Fiser 14 May '99

14 May '99

Dear Users, recently we got several questions personaly or on the list about the same problem: Modeller crashes because the template structures are not overlapping. This happens when for instance one tries to model a dimer using two different template structures for each of the domains and without any structural overlap between them. When the program starts, Modeller tries to superpose the two or more templates according to the alignmnet which does not work in these cases, of course, then stops with error. Despite of the missing information about the structural orientation of the templates you can do the modeling if you include in your top file the following modified subroutine, just as you see below: SUBROUTINE ROUTINE = 'transfer_xyz' # SET ALIGNMENT_FORMAT = 'PIR' ## READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS ## MALIGN3D FIT = off, GAP_PENALTIES_3D = 0 4 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUENCE READ_TOPOLOGY FILE = TOPLIB READ_PARAMETERS FILE = PARLIB CALL ROUTINE = 'create_topology' TRANSFER_XYZ CLUSTER_CUT = -1.0 BUILD_MODEL INITIALIZE_XYZ = OFF WRITE_MODEL FILE = MODEL RETURN END_SUBROUTINE Modeller will create models, but in case of insufficient implicit structural restraints (as e.g. bulkiness of the structures) the orientation of the individual, not overlapping parts of the model (as defined by the not overlapping templates) and the confomation of the interconnecting segments may be not accurate. Users may impose some knowledge for the orientation of the domains, by orienting the structures prior to the modelling, or if they can introduce explicit restraints in between the independent structural parts (e.g. catalytic site between units: upper limit distance restraints among catalytic residues etc.) Also, at the end of modelling , if the orientation of the templates was dubios one should not force the overall final superposition : set FINAL_MALIGN3D = 0 best wishes, Andras -- , Andras Fiser, PhD # phone: (212) 327 7206 The Rockefeller University # fax: (212) 327 7540 Box 270, 1230 York Avenue # e-mail:fisera@rockefeller.edu New York, NY 10021-6399, USA # http://salilab.org/~andras

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alignement error
by Michel Giorgi 14 May '99

14 May '99

Dear Modellers, I try to model my target protein on several templates (a big one and 6 very small ones), moreless as it is indicated in question 4 of the FACs. Unfortunately the program ends in error when checking the alignements, with the following error message: ################### fit2xyz_E> number of equivalent positions < 3: 0 recover__> MODELLER_STATUS >= STOP_ON_ERROR: 1 1 ################### My alignement file looks like this: >P1;temp1 structure:temp1: 45:: 356:: NECLGTIGPVTPLDASDFALDIRMPGVT-PKESDTYFCMSMRLPVD-EEAFVIDFKP--------RASMDTVHHMLL FGC----------------------------N--MPSSTGSYWFCDEGTCTDKAN----ILYAWARNAPPTRLPKGV GFRVGGETGSKYFVLQVHYGDI-----NHKDCSGVSVHLTRVPQPLIAGMYLMMSVDT---VIPPGEKVVNADISC- -----------QYKMYPMHVFAYRVHTHHLG-KVVSGYRVRNGQ-WTLIGRQN-------------------PQLP- -QAFYPVEHPVDVTFGDILAARCVFTGEGRTEATHIGGTSSDEMCNLYIMYYMEAKYALSFMTCTKNVAPDMFRTIP AEANIPIII* >P1;temp2 structure:temp2: 74:: 81:: ---------------------------------------------------------KVTEGSEQ* >P1;temp3 structure:temp3: 85:: 97:: ----------------------------------------------------------------------------- ---AAKIITHPNFNGN* >P1;temp4 structure:temp4: 17:: 30:: ----------------------------------------------------------------------------- ----------------CKHSMK-YRLSFCRK* >P1;temp5 structure:temp5: 258:: 269:: ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- ----------------------------------------------------------------------------P DWCTASGTPAS* >P1;temp6 structure:temp6: 75:: 93:: ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- -----------------------------------------------------KYVPHFKPGKELRDRANIY* >P1;temp7 structure:temp7: 30:: 47:: ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- ----------------------------------------------------------------------------- -----------------------------------------------------FHPPHI-EIQMLKNGKKIP* >P1;target sequence:target: LLKPSIPKPALPADTC--TMEIRAPDVLIPGQQTTYWCYVTELPDGFPRHHIVMYEPIVTEGNEA-----LV66MEV FQCAAEFRDHPHFSGPCDSKMKPQRLNFCRH----------------------------VLAAWALGAKAFYYPEEA GLAFGGPGSSRFLRLEV6YHNPLVIT-GRRDSSGIRLYYTAALRRFDAGIMELGLAYTPVMAIPPQETAFVLTGYCT DKCTQLALPAS-----GIHIFASQLHTHLTGRKVVTVL-ARDGRETEIVNRDNHYSPHFQEIRMLKKVVSVQ----- --------------PGDVLITSCTYNTEDRRLATVGGFGILEEMCVNYVHYYPQTQLEL----CKSAVDPGFLHKYF RLVNR--LL* Has anyone an idea about the problem? The error is the same if i only use the 2 first templates for instance. Thank you, regards. -- Michel GIORGI Lab. de Cristallochimie Faculte de St. Jerome Marseille, cedex 20, FRANCE

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Modeller and DEC Alphastations
by Stefano Pascarella +39 06 4991 7574 03 May '99

03 May '99

I am trying to run Modeller on a DEC alphastation but the program stops with the message: Insufficent memory to open Fortran RTL message catalog, message #41. I have already allocated an additional swap area. Could anybody with experience on Alphastation suggest a solution? Thanks in advance, Stefano Pascarella

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Problem with chimera model
by Tony Pemberton 27 Apr '99

27 Apr '99

Dear Users, I am trying to produce a chimeric model as in FAQ number 4. However I am getting the following error using Modeller release 4:- >> CHECK_ALIGNMENT: chkaln___> Checking pairwise structural superpositions: Equivalent CA pairs with distance difference larger than 6.0 angstroms: ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------------- chkaln___> Checking structure-sequence alignments: Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------- << end of CHECK_ALIGNMENT. fit2xyz_E> number of equivalent positions < 3: 2 recover__> MODELLER_STATUS >= STOP_ON_ERROR: 1 1 Can someone tell what this error means, Regards, Tony Pemberton ********************************************************************* Mr. A.J.Pemberton Tel: +121-414-3388 c/o Dept. Rheumatology, Fax: +121-414-3982 Medical School, E-mail: A.J.Pemberton(a)bham.ac.uk The University of Birmingham, Birmingham B15 2TT. U.K. *********************************************************************

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hydrogens in output structure
by Jiri Damborsky 26 Apr '99

26 Apr '99

Dear Modeller users: Is there any way how to generate homology model with hydrogen atoms included in the output structure. we tried using the template structure with hydrogens and 'SET HYDROGEN_IO = on' in the top file, but the output structure was again without hydrogens. Thank you very much for your advice. Best regards, Jiri * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Dr. Jiri Damborsky Laboratory of Biomolecular Structure & Dynamics Masaryk University Kotlarska 2 611 37 Brno Czech Republic e-mail: jiri(a)chemi.muni.cz phone: +420-5-41129 377 FAX: +420-5-41129 506 http://www.chemi.muni.cz/~jiri

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modelling conformation
by Holger Kremmin 26 Apr '99

26 Apr '99

Hi, I want to model several short peptides with a special conformation. The templates have the polyproline II conformation, but the model-sequences are far divergent from the template-sequence. How can I model peptides (8-18 aa) with a given conformation ?

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