- modeller_usage - salilab.org

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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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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27 Dec '00

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mapres & modeller on Origin2000
by Oliver Hucke 15 Dec '00

15 Dec '00

Dear modellers, I have added a large residue to the modeller topology - and parameter-files. When I try to read the modified topology file, modeller stops execution with the error message "increase mapres". Does this mean that my new residue contains too many atoms? (I guess so, because deleting a part of the new residue leads to normal execution of READ_TOPOLOGY). I need to consider the complete residue. What can I do? I would like to add another question: So far I have used a DEC Alpha workstation for my work with modeller, but I could get access to a SGI Origin 2000 parallel computer with 46 Mips R 10000 processors (Operating system: Irix 6.5.7). Does a version of modeller exist which is suitable for this machine. Or do I have to recompile the program for this computer? If so, is it worth the effort (I am not very experienced in that)? Could I perhaps solve the problem described above by recompilation of modeller? Any help is very much appreciated. Oliver. -- ******************************************* Oliver Hucke (Dipl. Chem.) Institut fuer Physikalische Chemie II Universitaet Freiburg Albertstr. 23a 79104 Freiburg Germany Tel.: ++49-761-203-6179 Fax : ++49-761-203-6189 email: hucke(a)uni-freiburg.de *******************************************

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A query
by S. Zarina 30 Nov '00

30 Nov '00

Hi! I need some info. Is it possible to use slackware for installalation of modeller4? If yes, then any particular version? Thanks, Sincerely, Shamshad Zarina

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phi/psi distribution in alpha region
by richard charles garratt 02 Nov '00

02 Nov '00

Dear modeller users, I have a question concerning the phi/psi distribution in the alpha region. The homology models which I generate seem to have a curious phi/psi distribution within the allowed alpha region. Almost all the residues within procheck's red region are sharply clustered into two peaks (one at the classical alpha helical angles of around -60, -40) and the other at the gamma region ( -90, 0). I often get a couple of minor lateral peaks as well. This is very different from crystal structures (including my template), where there is a more homogenous spread within the allowed region, although obviously showing a greater density of points towards -60, -40. I wonder why this happens and if I am doing something obviously stupid. It would seem that the sigmas on binormal restrainsts for phi/psis are very small. Can I easily adjust these values and what is the easiest way? This question is related to a similar one concerning proline phis angles which I note have a tendancy to drift away from -65. I have in the past used special restraints on all prolines in order to reduce sigma(phi) for which the default value seems to be rather generous. I would be most grateful for any comments/suggestions/help. Thanks, Richard Garratt University of Sao Paulo

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selenium parametrization
by Fabrizio Giordanetto 27 Oct '00

27 Oct '00

Hi, I got selenomethionines on a template structure and the program does not find selenium in topology library. Have you got selenium parametrized (radii...) or any suggestions in my next moves? thanks a lot. fab

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