April 1999 - modeller_usage

problem!
by Paola D'Alessio 15 Jun '01

15 Jun '01

Dear users, I am trying to produce a chimeric model for my protein. The first thing I want to do is to check the alignment I have. When I tell Modeller to execute the "check_alignment" command, I get the following message: rdpir___E> alignment sequence not found in PDB file: 1 ./pXXXX.pdb ####################################################################################################################################### The alignment I have is: >P1;pXXXX structureX:pXXXX:.::.::::: CKPMSNFRF-GENHAIMGVAFTWVMALACAAPPLVGWS--RYIPEGMQC-SCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTH--------QGSDFGPIFMTIPAFFAKTSAVYNPVIYIMM* >P1;pAveM structure:pAveM:2::211::::: -----------VRWAKLYSLVIWGCTLLLSSPMLV-----------------------------EVFTNMLLNVVGFLLPLSVITFCTMQ---------------------ERRATVLVLVVLLLFIICWLPFQISTFLDTL----------------VITQIASFMAYSNSCLNPLVYVIV* >P1;Ali2 sequence:Ali2:::::::: VKTMSMGRMRGVRWAKLYSLVIWGCTLLLSSPMLVFRTMKEYSDEGHNVTACVISYPSL---IWEVFTNMLLNVVGFLLPLSVITFCTMQIMQVLRNNEMQKFKEIQT---ERRATVLVLVVLLLFIICWLPFQISTFLDTLHRLGILSSCQDERIIDVITQIASFMAYSNSCLNPLVYVIV* ####################################################################################################################################### Perhaps, something is wrong with file names or PDB codes.(I stored the pdb files as pXXXX.pdb) Can somebody help me? Thank you very much, Paola -- dott. Paola D'Alessio (PhD student) Universita' degli Studi di Salerno Dipartimento Scienze Farmaceutiche via Ponte Don Melillo, 84084 Fisciano (Sa), Italy tel.+39 089 962822; e-mail: pdalessio(a)unisa.it

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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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atom type
by F. Zuccotto 22 Apr '99

22 Apr '99

Hello, I am trying to introduce a new molecule in to the top.lib library. I would like to know where I can find a description of the atom types used by modeller. Thanks fabio **************************** Fabio Zuccotto Biological NMR Centre Medical Sciences Building University Road Leicester LE1 9HN ENGLAND (UK) Tel. +44 (0)116 252 3071

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modeller for linux
by Gunnar Schotta 20 Apr '99

20 Apr '99

I want to use the modeller program on linux but ldd says that I need libf2c.so.0 Where can I get a binary of this library? I'm running Debian/GNU linux 2.1 (glibc2). Thank you!

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script file to obtain improved protein model?
by Antonello Romani 19 Apr '99

19 Apr '99

Dear users, I have set my input files to obtain an improved model of my protein. I wolud like to know if these files are right or wrong and if there are other stuff that I have to do to improve quality of my protein (I test it with Procheck or What_Check) ----------------------------------Build model--------------------------------------------------- # INCLUDE # Include the predefined TOP routines SET ALNFILE = 'xxxx.ali' # alignment filename SET SEQUENCE = 'myprot' SET LIBRARY_SCHEDULE = 1 SET MD_LEVEL = 'refine3' SET FINAL_MALIGN3D = 1 SET REPEAT_OPTIMIZATION = 15 SET RSTRS_REFINED = 2 SET MD_RETURN = 'MINIMAL' SET KNOWNS = 'template' # codes of the templates SET ATOM_FILES_DIRECTORY = 'xxxxxxxxxx' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 15 # Do a mixed minimization # Do homology modeling CALL ROUTINE = 'model' ------------------------------------------------------------------------------------------------ ----------------------------------Optimize stereochemistry-------------------------------------- # INCLUDE # Include the predefined TOP routines READ_TOPOLOGY FILE ='$(LIB)/top_heav.lib' READ_PARAMETERS FILE = '$(LIB)/par.lib' READ_MODEL FILE = 'myprot.pdb' SEQUENCE_TO_ALI ATOM_FILES = 'myprot.pdb', ALIGN_CODES= 'myprot' SEQUENCE_TO_ALI ADD_SEQUENCE = on,ATOM_FILES = ATOM_FILES 'myprot',ALIGN_CODES= ALIGN_CODES 'myprot' GENERATE_TOPOLOGY SEQUENCE = 'myprot' TRANSFER_XYZ BUILD_MODEL INITIALIZE_XYZ = off WRITE_MODEL FILE = 'myprot.ini' # GENERATE THE RESTRAINTS MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo' WRITE_RESTRAINTS FILE = 'myprot.rsr' ENERGY DYNAMIC_SPHERE = on SWITCH_TRACE TRACE_OUTPUT = 1, FILE = 'myprot.trc' ENERGY DYNAMIC_SPHERE = on OPTIMIZE DYNAMIC_LENNARD =on OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 10000 OPTIMIZE OPTIMIZATION_METHOD = 3, TEMPERATURE = 300, MAX_ITERATIONS = 10000,MD_RETURN = 'MINIMAL',EQUILIBRATE =20,; MD_TIME_STEP =2.0, CAP_ATOM_SHIFT = 0.1, RAND_SEED = -3065 OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 10000 ENERGY WRITE_MODEL FILE= 'myprot_optimize.pdb' ------------------------------------------------------------------------------------------------

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Re: modeller for linux
by Holger Kremmin 15 Apr '99

15 Apr '99

Look at http://rpmfind.net/linux/RPM/openlinux/1.3/col/contrib/RPMS/f2c-19960205-5. i386.html Be sure that the lib-directory is in the path. Holger Kremmin > ---------- >>Von: Gunnar Schotta <schotta(a)genetik.uni-halle.de> >>An: modeller_usage(a)salilab.org >>Betreff: modeller for linux >>Datum: Don, 15. Apr 1999 11:30 Uhr >> > >> I want to use the modeller program on linux but >> ldd says that I need libf2c.so.0 >> Where can I get a binary of this library? >> I'm running Debian/GNU linux 2.1 (glibc2). >> Thank you! >> >>

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