December 2000 - 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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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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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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