- modeller_usage - salilab.org

constraining an serine triade
by MarcoBocola 15 Mar '01

15 Mar '01

Hello from Marburg, I want to do homology modelling on serine hydrolases with highly conserved fold and reasonable AA-identity. So the difficulty is to model the active site correctly with respect to the catalytic triade and the backbone nitrogens in the oxyanion hole. These few amino acids should be overlayed as exact as possible. Is there a straightforward way to contstrain modeller only for these higly conserved topology of the catalytic residues within one Angstroem, thus remaining the catalytic hydrogen bond network intact. Any hints on possible protocolls appreciated. Marco

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Modeller4 on IRIX 6.5: additional versions available?
by Allen Smith 03 Feb '01

03 Feb '01

Hi. We're about to start using modeller4 on various IRIX 6.5 machines. These include r5000 (O2s and Indys) and r12000 (an Octane) processors. We are wondering whether the following could be made available: A. A version that will run properly on r12000 machines. These are using a later version of the r10000 processor, with both mips4 and 64-bit capabilities. The existing IRIX 6.5 r10000 versions will run only with a modification to the startup scripts of the LD_LIBRARY64_PATH variable adding /usr/lib64/mips4 to the start of that path. The reason this is necessary is that the -r10000 flag evidently used in compiling the r10000 versions of Modeller adds /usr/lib64/mips4/r10000 to the path of directories searched for libraries. This directory contains libfastm.so, which won't run on r12000 machines (I suspect it has assembler optimizations for r10000). Forcing rld (the runtime loader) to look at /usr/lib64/mips4 first causes it to instead use the more generalized mips4 version of libfastm.so. While this modification enables the tests to run properly, it qualifies as inconvenient and prone to bugs (especially if dealing with other programs such as InsightII that also set LD_LIBRARY64_PATH) and prone to bugs. A generalized mips4, 64-bit version of modeller4 should be compilable via adding: IRIX64 ) FC=f77; FFLAGS="-automatic -L/usr/lib64/mips4 -mips4 -64 -r8 -O2 -GCM:aggressive_speculation=ON -OPT:roundoff=3"; LDFLAGS="-L/usr/lib64/mips4 -Wl,-rpath,/usr/lib64/mips4 -lfastm" ;; \ to Makefile.include1. If it will work properly, f90 might be used instead of f77. -LNO and -IPA should enable better performance. B. A version that will run well on r5000 machines. These are 32-bit machines but will run mips4 code, which should improve modeller4's performance relative to the mips3 code which the existing IRIX n32-bit versions use. A generalized mips4, n32-bit version of modeller4 should be compilable via adding: mips4 ) FC=f77; FFLAGS="-automatic -L/usr/lib32/mips4 -mips4 -n32 -r8 -O2 -GCM:aggressive_speculation=ON -OPT:roundoff=3"; LDFLAGS="-L/usr/lib32/mips4 -Wl,-rpath,/usr/lib32/mips4 -lfastm" ;; \ to Makefile.include1. Again, if it will work properly, f90 might be used instead of f77, and -LNO and -IPA should enable better performance. In both of the above, specialized r5000 and r12000 versions would probably work even better. I don't know if you have either of these types of machines available to you. We are capable of such compilation ourselves but (obviously) don't have the modeller4 source code available to us. Thanks, -Allen -- Allen Smith easmith(a)beatrice.rutgers.edu

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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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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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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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