- modeller_usage - salilab.org

protein structure file (psf)
by Nitin Rathore 01 Feb '02

01 Feb '02

Hi, I am a new MODELLER user. I am interested in generating a structure file of the protein of my interest.I was wondering, if there is a way in MODELLER to write down a "CHARMM like .psf " file that lists all the bonds, bends, dihedrals, improper dihedrals etc ( for an all atom model, including hydrgens). Supposedly, the "BUILD MODEL" only generates the 3 D coordinates of the atoms in the model, based on the specified sequence of amino acid and the CHARMM topology and parameter file. But I can not figure out how to output a psf, structure file of my model protein. Looking for some help, Thanks in advance, Nitin

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RE: difference between version 4 and 6
by Andras Fiser 01 Feb '02

01 Feb '02

some dihedral angle libraries has improved, but in case of significant sequence similarity you will not see much effect of it. One difference, that the reference to the refinement protocoll has changed, earlier refine1 was the most exhaustive and refine 3 is the least, now it has changed and refine 3 is more exhaustive than refine2, and refine2 is more exhaustive than refine 1. Andras > -----Original Message----- > From: owner-modeller_usage(a)salilab.org > [mailto:owner-modeller_usage@salilab.org]On Behalf Of Luca > Settimo > Sent: Thursday, January 31, 2002 9:04 AM > To: 'Modeller Usage List' > Subject: difference between version 4 and 6 > > > Dear modellers, dear Andej Sali, > > I have one question for you. > I built several protein models using modeller 4 time ago... > I used in the top file the following parameters: > > SET HETATM_IO = on and off > SET WATER_IO = on and off > SET HYDROGEN_IO = off > SET STARTING_MODEL = 1 > SET ENDING_MODEL = 1 > SET MD_LEVEL = 'refine3' > CALL ROUTINE = 'model' > and I build the model with and without ligand and water in the binding > site... > > since the models that I built are quite a lot my question is: > > > do I have to expect some difference with the models obtained using the > new version (modeller 6 released the 25 January 2002) ... or do I have > to expect the same result? > for example does something differ when I model the ligand in the two > version? or just by using the same parameter in the top file above here? > > > > Thanks > > Luca > > ................................................................... > > Luca Settimo > Molecular Structures and Biocomputing > Department of Biochemistry and Pharmacy > Åbo Akademi University Tykistökatu 6A 20520 Turku Finland > phone: +358 (0) 2 2154600 > fax: +358 (0) 2 2153280 > mobile phone: +358 50 5238418 > mailto:lsettimo@abo.fi > http://www.abo.fi/~lsettimo > > > -- , Andras Fiser, PhD # phone: (212) 327 7216 The Rockefeller University # fax: (212) 327 7540 Box 270, 1230 York Avenue # e-mail:fisera@rockefeller.edu New York, NY 10021-6399, USA # http://salilab.org/~andras

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difference between version 4 and 6
by Luca Settimo 31 Jan '02

31 Jan '02

Dear modellers, dear Andej Sali, I have one question for you. I built several protein models using modeller 4 time ago... I used in the top file the following parameters: SET HETATM_IO = on and off SET WATER_IO = on and off SET HYDROGEN_IO = off SET STARTING_MODEL = 1 SET ENDING_MODEL = 1 SET MD_LEVEL = 'refine3' CALL ROUTINE = 'model' and I build the model with and without ligand and water in the binding site... since the models that I built are quite a lot my question is: do I have to expect some difference with the models obtained using the new version (modeller 6 released the 25 January 2002) ... or do I have to expect the same result? for example does something differ when I model the ligand in the two version? or just by using the same parameter in the top file above here? Thanks Luca ................................................................... Luca Settimo Molecular Structures and Biocomputing Department of Biochemistry and Pharmacy Åbo Akademi University Tykistökatu 6A 20520 Turku Finland phone: +358 (0) 2 2154600 fax: +358 (0) 2 2153280 mobile phone: +358 50 5238418 mailto:lsettimo@abo.fi http://www.abo.fi/~lsettimo

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SGI:segmentation fault
by Ada Prochnicka-Chalufour 31 Jan '02

31 Jan '02

Hello, Thanks a lot to Bozidar and Andras who kindly answered my question about 'memory requirements'. I have checked my parameters that seem to be big enough and I decided to have a look at things from the beginning, installing the recent modeller6v1. I still get a segmentation fault executing the tutorial examples (initial.top and model-defailt.top) with mod6v1_iris4d on my SGI Octane workstation ('trace' enclosed). Could you please tell me on which Silicon Graphics machine (which OS version) was modeller6 compiled? I would be grateful for any help. All the best, Ada ------------------------------------------------------------------------- balthus:adap 18>/ext5/usr/local/bin/modeller6v1/bin/mod6v1_iris4d initial MODELLER 6v1, 17 Jan 2002 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2002 Andrej Sali All Rights Reserved Written by A. Sali with help from A. Fiser, R. Sanchez, M.A. Marti-Renom, B. Jerkovic, A. Badretdinov, F. Melo, J.P. Overington & E. Feyfant Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, IRIX64 balthus 6.5 IP30 Date and time of compilation : 01/25/2002 20:36:35 Job starting time (YY/MM/DD HH:MM:SS): 2002/01/30 19:25:47.221 TOP_________> 2 2 READ_ALIGNMENT ALIGNMENT_FORMAT = 'PIR', FILE = 'alignmen; t.ali' openf5__224_> Open 11 OLD SEQUENTIAL alignment.ali openf5__224_> Open 11 OLD SEQUENTIAL alignment.ali Read the alignment from file : alignment.ali Total number of alignment positions: 106 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 5fd1 106 1 5fd1 ferredoxin 2 1fdx 54 1 1fdx ferredoxin TOP_________> 3 3 ID_TABLE MATRIX_FILE = 'id.mat' Segmentation fault ----------------------------------------------------------------------- and the second one: balthus:adap 29>$MODINSTALL6v1/bin/mod6v1_iris4d model-default MODELLER 6v1, 17 Jan 2002 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2002 Andrej Sali All Rights Reserved Written by A. Sali with help from A. Fiser, R. Sanchez, M.A. Marti-Renom, B. Jerkovic, A. Badretdinov, F. Melo, J.P. Overington & E. Feyfant Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, IRIX64 balthus 6.5 IP30 Date and time of compilation : 01/25/2002 20:36:35 Job starting time (YY/MM/DD HH:MM:SS): 2002/01/30 19:55:04.865 TOP_________> 105 705 SET ALNFILE = 'alignment.ali' TOP_________> 106 706 SET KNOWNS = '5fd1' TOP_________> 107 707 SET SEQUENCE = '1fdx' TOP_________> 108 708 SET ATOM_FILES_DIRECTORY = './:../atom_files' TOP_________> 109 709 SET STARTING_MODEL = 1 TOP_________> 110 710 SET ENDING_MODEL = 1 TOP_________> 111 711 CALL ROUTINE = 'model' TOP_________> 112 398 CALL ROUTINE = 'getnames' TOP_________> 113 508 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL' TOP_________> 114 509 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; ' TOP_________> 115 510 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE TOP_________> 116 511 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE TOP_________> 117 512 SET ROOT_NAME = SEQUENCE TOP_________> 118 513 RETURN TOP_________> 119 399 CALL ROUTINE = 'homcsr' TOP_________> 120 106 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE Dynamically allocated memory at amaxseq [B,kB,MB]: 2205269 2153.583 2.103 openf5__224_> Open 11 OLD SEQUENTIAL alignment.ali Dynamically allocated memory at amaxbnd [B,kB,MB]: 3882961 3791.954 3.703 openf5__224_> Open 11 OLD SEQUENTIAL alignment.ali Read the alignment from file : alignment.ali Total number of alignment positions: 106 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 5fd1 106 1 5fd1 ferredoxin 2 1fdx 54 1 1fdx ferredoxin TOP_________> 121 107 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND Segmentation fault ========================================================================

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Non-bonded clashes
by Derek Smith 29 Jan '02

29 Jan '02

Dear Modellers I'm trying to refine a model using MODELLER-6, using a basic top script and thorough MD/SA refinement, but I keep getting som unwelcome non-bonded clashes. Does anyone have any idea as to how I can remove them using MODELLER? Thanks in Advance, Derek Smith -- ************************************************************************ Dr. Derek Smith, Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York. YO10 5DD, United Kingdom. phone: (01904) 434532 fax: (01904) 410519 email: derek(a)ysbl.york.ac.uk ************************************************************************

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library error
by dkabic01 28 Jan '02

28 Jan '02

hi I am using modeller version 6.0 and I am getting this error message when it reads my alignment file: " lib-4194 : UNRECOVERABLE library error Encountered during a sequential formatted READ from an internal file (character variable) IOT Trap Abort (core dumped) " I would be highly obliged if somebody could guide me this problem bye dinesh

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sequence_search
by marco sette 28 Jan '02

28 Jan '02

Dear all, I'm new in using the modeller package. After downloading the program I started a simple top script both in a PC using linux (RedHat 7.0) or on a alpha station. In the first case the log file contains only normal informations about the program (modeller 6.v.0 ecc.) without the list of similar proteins; in the second one I have these two lines: read_se_367E>sequence not found; code: P1;xnb recover___E> ERROR_STATUS >= STOP_ON_ERROR : 1 1 the script is very simple SET SEARCH_RANDOMIZATIONS = 100 SET FILE = 'myseq.seq' SEQUENCE_SEARCH ALIGN_CODES = 'myseq', DATA_FILE = ON and I have the myseq.seq in the same directory. The .dat file is not generated. Does anyone has some suggestions ? Thanks for your help, bye, Marco ______________________________________________________________________ Dillo con una cartolina! http://it.greetings.yahoo.com/

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memory requirements
by Ada Prochnicka-Chalufour 28 Jan '02

28 Jan '02

Hello, I am getting my first experience with Modeller on an SGI Octane workstation running under IRIX 6.5 and here is the message I get when trying to execute the tutorial model-default.top: >...modeller6v0/src/main/mod6v0 model-default.top ...modeller6v0/src/main/mod6v0[41]: 13791 Memory fault What are the memory requirements for Modeller execution? Or, is the message actually about something else? Best regards, Ada ######################################################################## Ada Prochnicka-Chalufour, PhD. ada(a)pasteur.fr Unite de RMN des Biomolecules phone +33.1 40 51 30 85 Institut Pasteur, Paris, France ########################################################################

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Helix kink
by Dan Thomas Major 26 Jan '02

26 Jan '02

Hi, In my template protein there is a proline in a helix that causes a kink in the helix. This proline residue does not occur in the target protein,but modeller predicts a kink in the target protein as well. Should I "trust" modeller that there is likely to be a kink or is there a way of dealing with this... Thanks, Dan

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RE: reask
by Andrej Sali 24 Jan '02

24 Jan '02

Hi, Water is indicate by "w" in an alignment file and any one of HOH H2O OH2 MOH or WAT in a PDB file (cf modlib/restyp.lib). TIP3 is not a valid PDB file residue code, it is a 4 character CHARMM code (not the PDB code) for the water residue. PDB files use only 3 characters for residue codes, a CHARMM atom file may use up to 4 characters. The warning about the OH2 atom in the TIP3 residue was written out because the TIP3 PDB residue code is unknown to MODELLER. Still, probably the resulting model will not change much when you use the PDB water residue code instead of TIP3. All the best, Andrej -- Andrej Sali, Associate Professor The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399 tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540 e-mail sali(a)rockefeller.edu; http://salilab.org <http://salilab.org/> -----Original Message----- From: lsettimo(a)ra.abo.fi [mailto:lsettimo@ra.abo.fi] On Behalf Of Luca Settimo Sent: Monday, January 21, 2002 4:18 AM To: sali(a)rockefeller.edu Subject: reask Sorry if I reask, but for me it´s very important information. Thanks in advance if you can help me... Hello, I have one problem when I try to model water molecules. I check your FAQ and previous email... but I canno´t solve. I indicated water molecules 'w' in the alignment file, I edited my template (I replace HETATM with ATOM) like that in the end (using the right numeration of course also in the alignment): ATOM 1975 O BLK 263 78.930 33.505 36.595 1.00 20.17 or ATOM 1975 O TIP3 263 78.930 33.505 36.595 1.00 20.17 or ATOM 1975 O OH2 263 78.930 33.505 36.595 1.00 20.17 ... but in any case when I run modeller happens this: >> CHECK_ALIGNMENT: chkseq__E> sequence difference between alignment and pdb : STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*----- 1 260 28 TIP3 82 BLK KGECEw---- chkaln___> Checking structure-sequence alignments: Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------- 258 1 261 262 C E 25.243 << end of CHECK_ALIGNMENT. iatmcls_W> MODEL atom not classified: TIP3:OH2 patchss__> Number of disulfides patched in MODEL: 1 patchss__> Disulfide created between: 203 CYS 203 258 CYS 258 iatmcls_W> MODEL atom not classified: TIP3:OH2 In the end the model is created with the water (so it seems that everything work except this message) but why it writes like that? What I have to do to model the water (do I have to treat like BLK or like TIP3?) ................................................................... Luca Settimo Molecular Structures and Biocomputing Department of Biochemistry and Pharmacy Åbo Akademi University Tykistökatu 6A 20520 Turku Finland phone: +358 (0) 2 2154600 fax: +358 (0) 2 2153280 mobile phone: +358 50 5238418 mailto:lsettimo@abo.fi http://www.abo.fi/~lsettimo

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