- modeller_usage - salilab.org

Incorrect Topology library?
by Jeff Bush 24 Jun '05

24 Jun '05

Hello Experienced Modeller users, I am wondering if anyone has seen the following error message and has any idea what I need to do to fix the problem. I have seen this question asked before while searching the archives. It was asked previously in 2003 by Seth Goldenberg, but I do not see a response in the archives. Perhaps someone replied directly to this gentleman. I would certainly be very appreciative of any help you might provide. Error Message Follows. Thanks, Jeff Bush TOP_________> 132 89 READ_TOPOLOGY FILE = TOPLIB openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib//top_heav.lib openf5__224_> Open 11 UNKNOWN SEQUENTIAL ${MODINSTALL7v7}/modlib/models.lib TOP_________> 133 90 READ_PARAMETERS FILE = PARLIB openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib//par.lib Dynamically allocated memory at amattacns [B,kB,MB]: 6138979 5995.097 5.855 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL7v7}/modlib//par.lib rdparf__232_> parameters BONDS ANGLS DIHEDS IMPROPS MRFP MODE 227 561 661 112 0 0 TOP_________> 134 91 CALL ROUTINE = 'create_topology' TOP_________> 135 106 GENERATE_TOPOLOGY ADD_SEQUENCE = OFF act54___590E> No topology generated for sequence: Lk Possibly because incorrect topology library is used. recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1

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Terminal patching (acetylation/amidation) in Modeller 7.7
by Niels Johan Christensen 24 Jun '05

24 Jun '05

Dear all, First of all, thanks to Ben Webb for answering my question regarding acetylation in MODELLER 8.1. Now, I would like to do the same thing in MODELLER 7.7, but mod7v7.exe error terminates when I run my script. I have included my script and excerpt from the .log file below. It is rather peculiar that the .log says: ''Atom index is out of bounds: 708 706'', since these indices are indeed present in the .ini file. What goes wrong? Thank you. Best Regards, Niels Johan Christensen >>> My script <<< ------------------------------------------------------ INCLUDE SET PATCH_DEFAULT = off SET ALNFILE = 'VaLd-TRIL16C-HAND.PIR' SET KNOWNS = 'merged.pdb' SET SEQUENCE = 'TRIL16C' SET STARTING_MODEL = 1 SET ENDING_MODEL = 5 CALL ROUTINE = 'model' STOP SUBROUTINE ROUTINE = 'special_patches' PATCH RESIDUE_TYPE='ACE', RESIDUE_IDS='1:' PATCH RESIDUE_TYPE='CT2', RESIDUE_IDS='30:' RETURN END_SUBROUTINE ------------------------------------------------------- >>> The .LOG file <<<< getprog_531W> ROUTINE redefined: special_patches check_ali___> Checking the sequence-structure alignment. Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------- END OF TABLE delete__443_> Restraints marked for deletion were removed. Total number of restraints before, now: 6869 6678 csrrng__299E> Atom index is out of bounds: 708 706 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1

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Re: your message in Modeller user list.
by Ezequiel H Panepucci 24 Jun '05

24 Jun '05

drugdesign wrote: > Dear Ezequiel, > I've read your message in Modeller user list. I have similar problems on Suse 9.2 and also on Windows 2000. Have you solved these problems? > What was the cause of the problems? I had copied only the subdirectory automodel/ therefore all example data was missing and the program crashed instead of indicating "file not found". it is a bug which is fixed in the latest release. the problem could also happen due to stacksize limits, use "limit stacksize unlimited" if this is the case Zac > Respectively yours, > Adnrew Voronkov > > > I've recently installed Modeller 8v0 on Linux (Centos 4 which is derived from Redhat Enterprise Linux 4) and it is giving me a hard time. > > Below is what happens running examples/automodel/model-default.py. > > It happens using both the *tar.gz or *rpm installs. > > It gives similiar problems on Redhat 9 as well. > > > $ mod8v0 model-default.py > forrtl: severe (174): SIGSEGV, segmentation fault occurred > > Image PC Routine Line Source > libc.so.6 009F6B3D Unknown Unknown Unknown > mod8v0_i386-intel 0812A85D Unknown Unknown Unknown > mod8v0_i386-intel 08106CC8 Unknown Unknown Unknown > mod8v0_i386-intel 082A6647 Unknown Unknown Unknown > mod8v0_i386-intel 082A7E0A Unknown Unknown Unknown > mod8v0_i386-intel 082ED02E Unknown Unknown Unknown > mod8v0_i386-intel 08258A54 Unknown Unknown Unknown > mod8v0_i386-intel 082A5252 Unknown Unknown Unknown > mod8v0_i386-intel 082A7E0A Unknown Unknown Unknown > mod8v0_i386-intel 082A5ECD Unknown Unknown Unknown > mod8v0_i386-intel 082A7628 Unknown Unknown Unknown > mod8v0_i386-intel 082A7E0A Unknown Unknown Unknown > mod8v0_i386-intel 082A5ECD Unknown Unknown Unknown > mod8v0_i386-intel 082A7E0A Unknown Unknown Unknown > mod8v0_i386-intel 082A7FB6 Unknown Unknown Unknown > mod8v0_i386-intel 082C9800 Unknown Unknown Unknown > mod8v0_i386-intel 082CA0E6 Unknown Unknown Unknown > mod8v0_i386-intel 082CB1EB Unknown Unknown Unknown > mod8v0_i386-intel 080D40A7 Unknown Unknown Unknown > mod8v0_i386-intel 08076E94 Unknown Unknown Unknown > mod8v0_i386-intel 08076B2D Unknown Unknown Unknown > libc.so.6 009A1E33 Unknown Unknown Unknown > mod8v0_i386-intel 080769C1 Unknown Unknown Unknown > > -- Ezequiel PANEPUCCI, Ph.D. - Institut Pasteur Plate-Forme 6 - Cristallogénèse et Diffraction des Rayons X Telephone: +33 (0)1.4061.3930 Portable: +33 (0)6.1314.3906

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N-terminal acetylation via 'automodel?' ?
by Niels Johan Christensen 24 Jun '05

24 Jun '05

Dear all, I am a MODELLER newbie, modelling a synthetic peptide (3 chains * 30 AAs) from the 1COI.PDB entry. The results produced by the 'automodel' class are in many ways satisfactory, however I cannot figure out how to acetylate the amino terminus of the peptide. I acknowledge that this problem is adressed in the MODELLER FAQ, however the solution provided there does not seem to be designed for use with a simple 'automodel' script such as: from modeller.automodel import * env = environ() a = automodel(env, alnfile='vald-tril16c-hand.pir', knowns='merged.pdb', sequence='TRIL16C') a.starting_model = 1 a.ending_model = 5 a.make() Hence my question is: Will I have to abandon the use of the 'automodel' class and gain more insight into MODELLERs "fine structure" in order to change the default terminus patching ? Thank you. Best Regards, Niels Johan Christensen

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Homology model at specific pH
by Panapat Uawithya 23 Jun '05

23 Jun '05

Hi, I want to see the effect of the pH and the protein model. How can I model protein at specific pH. e.g. I want to see the + or - charge effect of histidine upon protein structure. Panapat --------------------------------- Yahoo! Mail Stay connected, organized, and protected. Take the tour

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not generating pdb files
by gerald.quon＠utoronto.ca 23 Jun '05

23 Jun '05

Hi, I'm running modeller 8v0, and am trying to model 2 different proteins on the same template. For some reason, for one of the alignments (#1), the only output being produced is the .D* and .V* files - the models aren't being generated (and the D* and V* files are being produced quite quickly). For alignment #2, I'm getting the models out so that isn't a problem. Any help would be appreciated...the same commands are being used for both alignments, which i've shown below.. Gerald ------------ script command: def my_model(_alnfile, _knowns, _sequence): log.verbose() #request verbose output env = environ() #create a new MODELLER environment to build model env.io.atom_files_directory = './:../pdb/' a = automodel (env, alnfile = _alnfile, knowns = _knowns, sequence = _sequence) a.starting_model = 1 a.ending_model = 50 a.final_malign3d = True a.md_level = refine.slow a.make() ----------- alignment #1: >P1;1PVM structureX:1PVM:FIRST:A:LAST :B:.:.: 0.00: 0.00 KIMNSNFKTVNWN-TTVFDAVKIMNENH----LYGLVVK--D---DNGN----DVGLLSE RSIIKRFIPRNKKPDEV------------------------------------------- ------------------------------------------------------------ -----------------------------------PIRLVMRKPIPKVKSDYDVKDVAAY LSENGLERCAVVDDPGRVVGIVTLTDLSRYLS/ KIMNSNFKTVNWN-TTVFDAVKIMNENH----LYGLVVK--D---DNGN----DVGLLSE RSIIKRFIPRNKKPDEV------------------------------------------- ------------------------------------------------------------ -----------------------------------PIRLVMRKPIPKVKSDYDVKDVAAY LSENGLERCAVVDDPGRVVGIVTLTDLSRYLS * >P1;a1 sequence:: : : : :::-1.00:-1.00 DIMVRDVPHVALS-CTFRDLRLALHRTK--GRMLALVES--P---ESMI----LLGSIER SQVVALLGAQLSPARRRQHMQERRATQTSPLSDQEGPPSPEASVCFQVNTEDSAFPAARG ETHKPLKPALKRGPSVTRNLGESPTGSAESAGIALRSLFCGSPPPEAASEKLESCEKRKL KRVRISLASDADLEGEMSPEEILEWEEQQLDEPVNFSDCKIDPAPFQLVERTSLHKTHTI FSLLGVDHAYVT-SIGRLIGIVTLKELRKAIE/ DIMVRDVPHVALS-CTFRDLRLALHRTK--GRMLALVES--P---ESMI----LLGSIER SQVVALLGAQLSPARRRQHMQERRATQTSPLSDQEGPPSPEASVCFQVNTEDSAFPAARG ETHKPLKPALKRGPSVTRNLGESPTGSAESAGIALRSLFCGSPPPEAASEKLESCEKRKL KRVRISLASDADLEGEMSPEEILEWEEQQLDEPVNFSDCKIDPAPFQLVERTSLHKTHTI FSLLGVDHAYVT-SIGRLIGIVTLKELRKAIE * ------------------------------ Alignment #2: >P1;1PVM structureX:1PVM:FIRST:A:LAST :B:.:.: 0.00: 0.00 KIMNSNFKTVNWN-TTVFDAVKIMNENH----LYGLVVK--D---DNGN----DVGLLSE RSIIKRFIPRNKKPDEV------------------------------------------- ------------------------------------------------------------ -----------------------------------PIRLVMRKPIPKVKSDYDVKDVAAY LSENGLERCAVVDDPGRVVGIVTLTDLSRYLS/ KIMNSNFKTVNWN-TTVFDAVKIMNENH----LYGLVVK--D---DNGN----DVGLLSE RSIIKRFIPRNKKPDEV------------------------------------------- ------------------------------------------------------------ -----------------------------------PIRLVMRKPIPKVKSDYDVKDVAAY LSENGLERCAVVDDPGRVVGIVTLTDLSRYLS * >P1;a2 sequence:: : : : :::-1.00:-1.00 RRNDPLLTVLTQDSMTVEDVETIISETT--YSGFPVVVS--R---ESQR----LVGFVLR RDLIISIENARKKQDGVV------------------------------------------ ------------------------------------------------------------ -------------STSIIYFTEHSPPLPPYTPPTLKLRNILDLSPFTVTDLTPMEIVVDI FRKLGLRQCLVT-HNGRLLGIITKKDVLKHIA/ RRNDPLLTVLTQDSMTVEDVETIISETT--YSGFPVVVS--R---ESQR----LVGFVLR RDLIISIENARKKQDGVV------------------------------------------ ------------------------------------------------------------ -------------STSIIYFTEHSPPLPPYTPPTLKLRNILDLSPFTVTDLTPMEIVVDI FRKLGLRQCLVT-HNGRLLGIITKKDVLKHIA *

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disulfide bonds
by Dmitry Osolodkin 23 Jun '05

23 Jun '05

Hi all, I have a little problem with Modeller 8v0. Usually it patches disulfide bonds automatically. But when I try to make model of my protein, it patches only one disulfide instead of five. When I try to define these bonds manually (like in FAQ p.3), the procedure stops and says: TypeError: special_patches() takes exactly 1 argument (2 given) .log file ends immediately. What can be the root of problem? Input files are here. The template is a protein with pdb id 1yi5, slightly minimized in Sybyl. When I use pdb id 1ux2 as a template, there are no problems, and disulfide bonds are on their place. >P1;1yi5_min structureX:1yi5_min:.:A:.:E: : : : LDRADILYN----IRQTSRPDV--IPTQRDRPVAVSVSLKFINILEVNE ITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVP--ISSLWVPDLAAYNAI S--KPEVLTP-QLARVVSDGEVLYMPSIRQRFSC--DVSGVDTESGATCRI KIGSWTHHSREISVDPT----SDDSEYFSQYSRFEILDVTQKKNSVTYSCC PEAYEDVEVSLNFRKKG-/ LDRADILYN----IRQTSRPDV--IPTQRDRPVAVSVSLKFINILEVNE ITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVP--ISSLWVPDLAAYNAI S--KPEVLTP-QLARVVSDGEVLYMPSIRQRFSC--DVSGVDTESGATCRI KIGSWTHHSREISVDPTT-N-SDDSEYFSQYSRFEILDVTQKKNSVTYSCC PEAYEDVEVSLNFRKKG-/ LDRADILYN----IRQTSRPDV--IPTQRDRPVAVSVSLKFINILEVNE ITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVP--ISSLWVPDLAAYNAI S--KPEVLTP-QLARVVSDGEVLYMPSIRQRFSC--DVSGVDTESGATCRI KIGSWTHHSREISVDPT----SDDSEYFSQYSRFEILDVTQKKNSVTYSCC PEAYEDVEVSLNFRKKGR/ LDRADILYN----IRQTSRPDV--IPTQRDRPVAVSVSLKFINILEVNE ITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVP--ISSLWVPDLAAYNAI S--KPEVLTP-QLARVVSDGEVLYMPSIRQRFSC--DVSGVDTESGATCRI KIGSWTHHSREISVDPTTEN-SDDSEYFSQYSRFEILDVTQKKNSVTYSCC PEAYEDVEVSLNFRKKG-/ LDRADILYN----IRQTSRPDV--IPTQRDRPVAVSVSLKFINILEVNE ITNEVDVVFWQQTTWSDRTLAWNSSHSPDQVSVP--ISSLWVPDLAAYNAI S--KPEVLTP-QLARVVSDGEVLYMPSIRQRFSC--DVSGVDTESGATCRI KIGSWTHHSREISVDPT--N-SDDSEYFSQYSRFEILDVTQKKNSVTYSCC PEAYEDVEVSLNFRKKG-/ * >P1;r1 sequence:r1:.:A:.:E: : : : PDITKSPLTKSEQLLRIDDHDFSMRPGFGGPAIPVGVDVQVESLDSISE VDMDFTMTLYLRHYWKDERLSFPSTNNLSMTFDGRLVKKIWVPDMFFVHSK RSFIHDTTTDNVMLRVQPDGKVLYSLRVTVTAMCNMDFSRFPLDT-QTCSL EIESYAYTEDDLMLYWKKGNDSLKTDERISLSQFLIQEFHTTTKLAFYSS- TGWYNRLYINFTLRRHI/ PDITKSPLTKSEQLLRIDDHDFSMRPGFGGPAIPVGVDVQVESLDSISE VDMDFTMTLYLRHYWKDERLSFPSTNNLSMTFDGRLVKKIWVPDMFFVHSK RSFIHDTTTDNVMLRVQPDGKVLYSLRVTVTAMCNMDFSRFPLDT-QTCSL EIESYAYTEDDLMLYWKKGNDSLKTDERISLSQFLIQEFHTTTKLAFYSS- TGWYNRLYINFTLRRHI/ PDITKSPLTKSEQLLRIDDHDFSMRPGFGGPAIPVGVDVQVESLDSISE VDMDFTMTLYLRHYWKDERLSFPSTNNLSMTFDGRLVKKIWVPDMFFVHSK RSFIHDTTTDNVMLRVQPDGKVLYSLRVTVTAMCNMDFSRFPLDT-QTCSL EIESYAYTEDDLMLYWKKGNDSLKTDERISLSQFLIQEFHTTTKLAFYSS- TGWYNRLYINFTLRRHI/ PDITKSPLTKSEQLLRIDDHDFSMRPGFGGPAIPVGVDVQVESLDSISE VDMDFTMTLYLRHYWKDERLSFPSTNNLSMTFDGRLVKKIWVPDMFFVHSK RSFIHDTTTDNVMLRVQPDGKVLYSLRVTVTAMCNMDFSRFPLDT-QTCSL EIESYAYTEDDLMLYWKKGNDSLKTDERISLSQFLIQEFHTTTKLAFYSS- TGWYNRLYINFTLRRHI/ PDITKSPLTKSEQLLRIDDHDFSMRPGFGGPAIPVGVDVQVESLDSISE VDMDFTMTLYLRHYWKDERLSFPSTNNLSMTFDGRLVKKIWVPDMFFVHSK RSFIHDTTTDNVMLRVQPDGKVLYSLRVTVTAMCNMDFSRFPLDT-QTCSL EIESYAYTEDDLMLYWKKGNDSLKTDERISLSQFLIQEFHTTTKLAFYSS- TGWYNRLYINFTLRRHI/ * # Homology modelling by the automodel class from modeller.automodel import * # Load the automodel class log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = './' a = allhmodel(env, alnfile = 'align.ali', # alignment filename knowns = '1yi5_min', # codes of the templates sequence = 'r1') # code of the target # Very thorough VTFM optimization: a.library_schedule = 1 a.max_var_iterations = 300 # Very thorough MD optimization: a.md_level = refine.very_slow # Repeat the whole cycle 3-times and do not stop unless obj.func. > 1E6 a.repeat_optimization = 3 a.max_molpdf = 1e6 a.make() # do the actual homology modelling

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Modeller 8v1 release
by Modeller Caretaker 22 Jun '05

22 Jun '05

The new version of Modeller, 8v1, is now available for download from http://salilab.org/modeller/. If you have a license key for Modeller 8v0 or 7v7, there is no need to reregister for Modeller 8v1 - the same license key will work. (It won't do any harm to reregister if you want to, though!) If you encounter bugs in Modeller 8v1, please see http://salilab.org/modeller/manual/node11.html for information on how to report them. New features in Modeller 8v1 include: # Removal of limits on the number of pseudo atoms, segments, the length of file names and most other strings, and the number of parameters in parameter files. # Removal of the read_restyp() command. To read a user-defined residue type file, set restyp_lib_file when creating an environ object. # Bug fix: the correct VDW radii (as selected by topology.submodel) are now used for PSA calculations (previously the all-hydrogen radii were used in all cases). # Improved error handling: almost all errors should be recoverable now (using the standard Python exception handling mechanism) and incorrect input should trigger an error rather than causing Modeller to crash (please report any crashes as bugs to the developers). # SALIGN bug fixes, improved binning of access classes. # Modeller scripts are now more like 'real' Python scripts; the PYTHONPATH environment variable is honored, and additional command line arguments can be given to your scripts (accessible as sys.argv). # Bug fix for alignment.segment_matching(): correct alignment scores are now written. # Support for AMD64 and EM64T (Opteron/Xeon64) Linux machines. # DOPE model assessment now returns only the DOPE energy itself by default, ignoring other energy terms. # Bug fix for model.restraints.pick() when used with absolute position restraints; always allow 1-atom restraints to pass the residue_span_range check. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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Pick Restraints
by John Penniston 16 Jun '05

16 Jun '05

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problems with modeller
by limongelli＠unina.it 16 Jun '05

16 Jun '05

To whom it may concern, I'm a researcher of Naples University and I'm using modeller for my work. I've followed correctly the Basic tutorial with my enzyme in the place of lactate dehydrogenase. The program run but I got many warnings in the following .log files: 1) when I run "mod8v0 compare.py" I got this warning: fndatmi_285W> Number of residues <> number of atoms; atom code: 680 679 CA 2) when I run "mod8v0 align2d.py" I got these warnings: iup2crm_280W> No topology library in memory or assigning a BLK residue. Default CHARMM atom type assigned: N --> N This message is written only for the first such atom. fndatmi_285W> Number of residues <> number of atoms; atom code: 680 679 CA fndatmi_285W> Number of residues <> number of atoms; atom code: 680 679 CA 3) when I run "mod8v0 model-single.py" I got these warnings: fndatmi_285W> Number of residues <> number of atoms; atom code: 680 679 CA getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 275 atom names : C +N atom indices : 2252 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 10 275 atom names : C CA +N O atom indices : 2252 2247 0 2253 fndatmi_285W> Number of residues <> number of atoms; atom code: 680 679 CA omgdel__425W> Unselected all O C +N +CA dihedrals: 282 mdtrsr__446W> A potential that relies on one protein is used, yet you have at least one known structure available. MDT, not library, potential is used. delete__443_> Restraints marked for deletion were removed. Total number of restraints before, now: 21721 19723 iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. iupac_m_397W> Atoms were not swapped because of the uncertainty of how to handle the H atom. Could someone please help me to find where I did wrong Thanks in advance Vittorio ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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