April 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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linux installation problem
by Daniel John Rigden 25 Apr '01

25 Apr '01

Hi Everyone Can anyone help with an intallatin problem I'm having? My machine is a PIII 933 running RH7.0. The installation of both f2c and modeller seem to go fine but then when I type mod I get the following /usr/local/bin/modeller4/bin/mod_i386: error while loading shared libraries: libc.so.5: invalid ELF header As a linux novice this means nothing to me. Thanks in advance for your help. Daniel Rigden +-------------------------------------------------------------------------+ | Dr Daniel John Rigden | | CENARGEN/EMBRAPA | e-mail: daniel(a)cenargen.embrapa.br | | Parque Estacao Biologica | http://www.cenargen.embrapa.br | | PqEB - Final - Av. W3 Norte | Phone: +55 (61)448-4741 | | 70770-900, Brasilia-D.F.-BRAZIL | Fax: +55 (61)340-3658 | +-------------------------------------------------------------------------+

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linux installation problem
by Oliver Hucke 19 Apr '01

19 Apr '01

Dear All, I am trying to install modeller4 on a new PC with Suse linux7.1. After correction of the default HOSTTYPE setting (for some reason it is set to "i386-linux" on my machine instead of "i486-linux"), the "Install" script finishes surprisingly fast (may be due to the 1.2GHz CPU) and without any error messages. Afterwards, modeller can be started (execution of "mod4" without any argument), but when I try to execute the tutorial test cases ("/tutorial-model/run_tops1") I am receiving the following error message from every top-script: /usr/local/bin/modeller4/bin/mod_i486-linux: error while loading shared libraries: /usr/local/bin/modeller4/bin/mod_i486-linux: undefined symbol: acos Execution is terminated and the log files of the scripts are completely empty. Does anybody know, what this means and how to avoid it? Thank you very much! Oliver. ******************************************* Oliver Hucke 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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spline restraints
by Evers Andreas 18 Apr '01

18 Apr '01

Hello! I want to do homology modelling including information from ligands to model the active site of a protein. I started with hemoglobin as the heme substrate and its topology are already defined in the Modeller4 libraries. As restraints I want to use knowledge based pair potentials between protein and ligand atoms derived from complexes in the PDB and express these restraints as splines. In the top-file, I include the following SPECIAL_RESTRAINTS routine: ######################### SUBROUTINE ROUTINE = 'special_restraints' SET DYNAMIC_MODELLER = on SET CONTACT_SHELL = 6.00 READ_ATOM_CLASSES ATOM_CLASSES_FILE = 'atmcls-special.lib' READ_PARAMETERS FILE = 'special-pairpot.lib', ADD_PARAMETERS = on END_SUBROUTINE ######################### In the file "atmcls-special.lib" I grouped the protein atoms (ATMGRP A001 - A012) and the HEME atoms (A041 - A058) according to SYBYL atom classifications. In the file "special-pairpot.lib" I try to express these pair-potentials as splines. The file looks like this: ######################### MODELLER12 VERSION: USER FORMAT R 10 25 1 31 2 31 0 A001 A041 1.0 0.0 6.0 0.25 -0.05 0.05 values R 10 25 1 31 2 31 0 A002 A041 ... . . . ######################### When I run Modeller it reads the "special-pairpot.lib"-file but then tells me "rdparf__E > increase MATTACNS" and exits. Does anyone know what went wrong? I am not sure if my parameters in the "special-pairpot.lib"-file are set correctly. Thank you very much for your help, Andreas -- ###################################################################### # Andreas Evers # # # # Research group for Drug Design & X-ray Crystallography # # Institute of Pharmaceutical Chemistry # # Philipps-University of Marburg # # Marbacher Weg 6 phone2 +49-6421-28-25072 # # D-35032 Marburg FAX: +49-6421-28-28994 # # email: Andreas.Evers(a)mailer.uni-marburg.de # # AG-Klebe-Home: http://www.agklebe.de # ######################################################################

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constraints
by Giulio Rastelli 07 Apr '01

07 Apr '01

Dear modellers, is it possible with Modeller4 to define constraints instead of restraints? I would like to constraint a set of conserved residues to be exactly in the same position as those of the template structure, and was looking for a way to do this without setting explicit distance, angle and torsion restraints. Thank yuo very much, Giulio Rastelli Dipartimento di Scienze farmaceutiche Universita di Modena , Italy

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Cyclic peptide...
by Erika Svangard 03 Apr '01

03 Apr '01

Dear Modellers, I'm trying to generate a model of a cyclic peptide based on a NMR structure of a cyclic peptide. I belive my alignment is fine as all disulfide bonds are conserved, but I wish to patch the N and C termini with a peptide bond. Please, could you suggest how I would do this? I have tried using the link special patch as shown below, but it is not working. I'm not sure if this is correct. I also tried with the reisdue IDs in the opposite order ('29' '1'), but without any luck. I would like your advice. Yours Erika Svangard SUBROUTINE ROUTINE = 'special_patches' PATCH RESIDUE_TYPE = 'LINK', RESIDUE_IDS = '1' '29' RETURN END_SUBROUTINE

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