January 2001 - modeller_usage

Error using MALIGN3D
by Michael Buck 24 Jan '02

24 Jan '02

MALIGN3D Top files which worked well using Modeler 4 are giving me this error : fndatmi_284E> Beginning atom index for a residue out of bounds: 0 0 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 I am using the following script # MALIGN3D READ_ALIGNMENT FILE = 'pair.aa' SET ATOM_FILES = '1.pdb' '2.pdb' SET FIT_ATOMS = 'CA' MALIGN3D GAP_PENALTIES_3D= 0 2.0, WRITE_FIT = on, WRITE_WHOLE_PDB = off If anybody has seen this problem, please help. Thank you Michael Buck ************************************************ Michael Buck NCSU Genetics mjbuck(a)unity.ncsu.edu Phone (919)515-5759 Fax (919)515-3355 http://www4.ncsu.edu/~mjbuck *************************************************

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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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Re: start up problem
by govind＠bic.nus.edu.sg 30 Jan '01

30 Jan '01

Dear All, When I exectute the top command file, its not running the modeller. Its reporting the following errors. Please clarify my doubts. Thanks in advance govind. ipdbnam_W> environment variable PBNET undefined >> CHECK_ALIGNMENT: rdpdb___E> no atoms read from the input PDB file; probably because segment specified incorrectly in the alignment file or in MODEL_SEGMENT; beginning residues number/chain id probably not found: 1 chkseq__E> Number of residues in the alignment and pdb files for alignment entry: 1 fndatmi_E> residue atom index out of bounds; ******

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modelisation problem
by Stephane Vandevuer 24 Jan '01

24 Jan '01

Dear MODELLER users, I have a problem using the program. I'm building a model of a chimeric protein which consists of a big protein (> 2000 residues) with an insertion of a smaller one (25 residues). There is a template for each of the those two proteins, and I chose anchors points too. The alignement file seems thus : proteinA aaaaaaaaaaaaaaaaaaaaaaaaaaa-----------------aaaaaaaaaaaaaaaaaaaaaaa proteinB -------------------------bbbbbbbbbbbbbbbbbbbbb--------------------- chimera aaaaaaaaaaaaaaaaaaaaaaaaaxxbbbbbbbbbbbbbbbbbxxaaaaaaaaaaaaaaaaaaaaa When I look to the .ini file, I can see that a part of the proteinB is close of a loop of the proteinA. In all the generetad models, the proteinB part moved away and the loop of the proteinA did'nt move at all. Is there an explanation ? Is it possible to make both moving ? Thank you in advance.

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by itoffers＠yahoo.com 21 Jan '01

21 Jan '01

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dihedral restraints
by Isabelle Ortmans 12 Jan '01

12 Jan '01

Hi, we are trying to generate 3D-models for a short peptide, on the basis of two template structures. We would like to restrain the mainchain dihedral angles in the central region of our peptide during the modelling procedure. To do this, we tried to modify the following input file which allowed us to use the 'model' routine and some special restraints at the same time. ======================================================================= #Homology modelling by the MODELLER TOP routine 'model'. INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 2 2 2 2 2 SET ALNFILE = 'ali1.pir' # alignment filename SET KNOWNS = 'sero_c' 'sero_o' # codes of the templates SET SEQUENCE = 'agen7' #code of the target SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model CALL ROUTINE = 'model' # do homology modelling STOP SUBROUTINE ROUTINE = 'special_restraints' SET ADD_RESTRAINTS = on MAKE_RESTRAINTS RESTRAINT_TYPE = 'strand', RESIDUE_IDS = '3' '6' RETURN END_SUBROUTINE ========================================================================== We thought it would be possible to modify the 'special_restraints' routine on the basis of the example file enforcing a cis conformation for a proline residue: =========================================================================# Example for: ADD_RESTRAINT, DELETE_RESTRAINT # This will enforce cis conformation for Pro-56. # Make a model and stereochemical restraints: DEFINE_STRING VARIABLES = ATOM_IDS1 ATOM_IDS2 READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib' READ_PARAMETERS FILE = '$(LIB)/par.lib' READ_MODEL FILE = '1fas' SEQUENCE_TO_ALI ATOM_FILES = '1fas', ALIGN_CODES = '1fas' SEQUENCE_TO_ALI ADD_SEQUENCE = on, ATOM_FILES = ATOM_FILES '1fas.ini', ; ALIGN_CODES = ALIGN_CODES '1fas-ini' GENERATE_TOPOLOGY SEQUENCE = '1fas-ini' TRANSFER_XYZ BUILD_MODEL INITIALIZE_XYZ = off MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo' # Change the Pro-56 restraint from trans to cis: CALL ROUTINE = 'cispeptide', ATOM_IDS1 = 'O:56' 'C:56' 'N:57' 'CA:57', ; ATOM_IDS2 = 'CA:56' 'C:56' 'N:57' 'CA:57' WRITE_RESTRAINTS FILE = '1fas.rsr' ENERGY SUBROUTINE ROUTINE = 'cispeptide' # Delete the old restraint on the same atoms: DELETE_RESTRAINT ATOM_IDS = ATOM_IDS1 # Add the new restraint: ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 3 3 4 2 0 3.141593 0.087 DELETE_RESTRAINT ATOM_IDS = ATOM_IDS2 ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 3 3 4 2 0 0.0 0.087 RETURN END_SUBROUTINE ========================================================================= Doing this, we succeeded in writing the correct restraints file, but the 'model' routine stopped and no new model was generated. We thought maybe it might be necessary to proceed in two steps: 1. writing the restraints file 2. reading this restraint file prior to run the 'model' routine. Any help or suggestion would be appreciated. Thank you Isabelle

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error message
by Giulio Rastelli 12 Jan '01

12 Jan '01

Hi, I got this error message while running modeller: fit2xyz_E> number of equivalent positions < 3: 0 recover__> MODELLER_STATUS >= STOP_ON_ERROR: 1 1 THE .TOP FILE IS: # Very fast homology modelling by the MODELLER TOP routine 'model'. INCLUDE # Include the predefined TOP routines SET ALNFILE = 'motilin_giulio4.align' # alignment filename SET KNOWNS = '1f88' '2EIA' # codes of the templates SET SEQUENCE = '1mot' # code of the target SET ATOM_FILES_DIRECTORY = '/lab/giulio/KOSAN/motilin/homology' SET STARTING_MODEL = 1 SET ENDING_MODEL = 1 CALL ROUTINE = 'model' # do homology modelling THE ALIGNMENT IS: >P1;1mot sequence:1mot: 1: : 412: :6a684b4cd3365f9a226ebadbae3b60b3MGSPKTMG 6-386::-1.00:-1.00 MGSPWNGSDGPEGAREPP---WPALPPCDERRCSPFPLGALVPVTAVCLCLFVVGVSGNVVTVMLIGRYRDMRTT TNLYLGSMAVSDLLILLGLPFDLYRLWRSRPWVFGPLLCRLSLYVGEGCTYATLLHMTALSVERYLAICRPLRAR VLVTRRRVRALIAVLWAVALLSAGPFLFL----------------------------VGVEQDPGISVVPGLNGT ARIASSPLASSPPLWLSRAPPP-----SPPSGPETAEAAALFSRECRPSPAQLGALRVMLWVTTAYFFLPFLCLS ILYGLIGRELWSSRRPLRGPAASGRERGHRQTVRVLLVVVLAFIICWLPFHVGRIIYINTEDSRMMYFSQYFNIV ALQLFYLSASINPILYNLISKKYRAAAFKLLLARKSRPRGFHRSRDTAGEVAGDTGGDTVGYTETSANVKTMG* >P1;1f88 structureX:1f88: 1:A: 328:A:1-332::-1.00:-1.00 ----MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTP LNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSN- FRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNES------------------ ---------------------------------------------------------FVIYMFVVHFIIPLIVIF FCYGQLVFTVKEAAA----SATT--QKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQG---SDFGPIFMTI PAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNP-------------------STTVSKTETSQVAPA--* >P1;2EIA structureX:2EIA: 52:A: 99:A:unknown:unknown:-1:-1 --------------------------------------------------------------------------- --------------------------------------------------------------------------- ------------------------------------------------------------EMNAFLDVVPGQAGQ KQILLDAIDKIADDWDNRHPLPNAPLVAPPQGP------------------------------------------ --------------------------------------------------------------------------- -------------------------------------------------------------------------* What does the error mean? The alignment seems to be ok... Thank you very much for your help Giulio Rastelli

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