July 2003 - modeller_usage

Modeller input alignment file
by christos Kouriniadis 26 Jan '04

26 Jan '04

Hello everybody, I am doing a project on comparative modelling, by using modeller. My problem is the following: I am trying to make an input file with PDB structures aligned in PIR format. However, when I am reading the modeller manual, I see that the worked example is in the form: P1;2ald structureX:2ald:2:@:363:@:aldolase:human muscle:2.00:0.17 * If you go to the section "display/download file", in the PDB website, you will get the usual big file. But when I have a look at this file, I see that ATOM has three coordinates: -20.521 45.890 70.464 How from these coordinates I get the :2:@:363:@: ??? Is there a formula that transforms it? I would be grateful if you could give me a hint on this. Thanks, Christos Kouriniadis _________________________________________________________________ Add photos to your e-mail with MSN 8. Get 2 months FREE*. http://join.msn.com/?page=features/featuredemail

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Attempting to run the first tutorial
by Andrew Latos 31 Jul '03

31 Jul '03

Dear MODELLER users, I installed modeller onto my computer. It looks as though I am having problems getting the program to run properly. I am running the program using bash instead of csh. In the installation, I accepted all defaults except for the program location. The program is located in a directory named /modeller. The program then can be found in /modeller/bin/mod6v2. Running the tutorial files included in the installation seem to work. I think that model-default.top is working properly. The problem comes when I attempt to run the tutorials from http://salilab.org/modeller/user_manual.shtml. The first tutorial generates this message: $ mod6v2 seq_search.top /modeller/bin/mod6v2: line 38: 1360 Killed $NICE ${EXECUTABLE} $STEERF >$LOGF The seq_search.top file looks like this: SET SEARCH_RANDOMIZATIONS = 100 SEQUENCE_SEARCH FILE = 'TvLDH.ali', ALIGN_CODES = 'TvLDH', DATA_FILE =ON I read that going into emacs and saving it may clear up the problem, but it did not. The output file seq_search.log starts off well I think. But I don' t know if the end is correct. It aligns over 800 sequences. From the .top file, I thought it would only align 100 sequences. Here is the start: MODELLER 6v2, 17 Feb 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, Linux dhcppc2 2.4.18-14 i686 Date and time of compilation : 07/16/2002 11:42:16 Job starting time (YY/MM/DD HH:MM:SS): 2003/07/28 22:20:50.755 seqsearc_> 1 TvLDH 1xnb 335 185 63 18.81 34.05 117083.50 _aln.pos 10 20 30 40 50 60 TvLDH MSEAAHVLITGAAGQIGYILSHWI-ASGELYGDRQVYLHLLDIPPAMNRLTALTMELEDCAFPHLAGF 1xnb ASTDYWQNWT-DGG--G-IVNA-VNGSG---GN---Y----SV----N-WSN-T-G--N--F--VVG- _consrvd * * * * * ** * * * * * * _aln.p 70 80 90 100 110 120 130 TvLDH VATTDPKAAFKDIDCAFLVASMPLKPGQVRADLISSNSVIFKNTGEYLSKWAKPSVKVLVIGNPDNTN 1xnb ------KG-WT----T---GS-PF-----RT--I--N---Y-NAG--V--WA-PN------GN-GY-- _consrvd * * * * * * * * ** * ** _aln.pos 140 150 160 170 180 190 200 TvLDH CEIAMLHAKNLKPENFSSLSMLDQNRAYYEVASKLGVDVKDVHDIIVWGNHGESMVADLTQATFTKEG 1xnb --LT-LYGWT-R----SPL--IE----YY-V-----VD--S------WGTY--R--P--T-GTY-K-G _consrvd * * * ** * ** ** * * * * _aln.pos 210 220 230 240 250 260 270 TvLDH KTQKVVDVLDHDYVFDTFFKKIGHRAWDILEHRGFTSAASPTKAAIQHMKAWLFGTAPGEVLSMGIPV 1xnb -TVKS-DGGTYD-IYTT--TRYN--APSI-D--G--DR-T-T-FT-QY---W---SV-RQ--S-K--R _consrvd * * * * * * * * * * * * _aln.pos 280 290 300 310 320 330 TvLDH PEGNPYGIKPGVVFSFPCNVDKEGKIHVVEGFKV-NDWLREKLDFTEKDLFHEKEIALNHLAQGG 1xnb PTGSN-A-T--ITFT-N-HVNA-WKSH---GMNLGSNWAYQVMA-TE-G-YQSSG-SSN-VTVW- _consrvd * * * * * * * * ** * It continues on until this point. _aln.pos 280 290 300 310 320 330 TvLDH EGNPYGIKPGVVFSFPCNVDKEGKIHVVEGFKVNDWLREKLDFTEKDLFHEKEIALNHLAQGG 1ayaA Q---Y-------Y-----M--E-H-H---G-Q----LKEK-N--G-DVI-ELKYPLN------ _consrvd * * * * * ** * * ** seqsearc_> 897 TvLDH 1az4A 335 187 77 22.99 41.18 123537.50 _aln.pos 10 20 30 40 50 60 TvLDH MSEAAHVLITGAAGQI-GYILSHWIASGELYGDRQVYLHLLDIPPAMNRLTALTMELEDCAFPHLAGF 1az4A -SLRSD-LIN-ALYDVCG-IIS---A--E--G-K-IY------P-----LSTI-FEL----FS-RP-I _consrvd * ** * * * * * * * * * * ** * (Fundamental)--L32747--Bot----------------- This leads me to think that it went over its 100 alignment limit and ended up timing out. I'm not sure how many hours this took. I believe it was over four hours. As you can see, the output file is 32 747 lines long. Here is what the install program included with the .bashrc file. I've removed the key in case you don't want it displayed in the forum. ### begin MODELLER6v2################################################## MODINSTALL6v2=/modeller EXECUTABLE_TYPE6v2=i386-absoft LIBS_LIB6v2=$MODINSTALL6v2/modlib/libs.lib KEY_MODELLER6v2=xxx mod=mod6v2 export MODINSTALL6v2 EXECUTABLE_TYPE6v2 LIBS_LIB6v2 KEY_MODELLER6v2 mod PATH=$PATH:$MODINSTALL6v2/bin ulimit -S -s unlimited ### end MODELLER6v2#################################################### My computer has a 500 mb swap file. I don't know if that is adequate or if it is not enough for this program. Perhaps I am missing another setting of some sort. Your help would be much appreciated. I've been trying to get the program to work for over a week so I'm perplexed. Thanks Andrew L University of Idaho ;-)

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Error in launching Modeller
by Antonio Arroyo Luque 30 Jul '03

30 Jul '03

Hello everybody, I'm a new user of Modeller, and I'm trying to launch it for the first time. First of all, I have to admit I'm not so familiar with programming languages, and perhaps this is the main problem with me. Anyway, I will very appreciate your patience and your valuable help and expertise. In my first attempt, I downloaded Modeller6v2 for Linux. It didn't work to me. As I'm not familiar with Linux either, I decided to download de Windows version of the program. I've installed it in a PC running Windows 2000 Pro with NT technology, and after modifying "modenv.bat" and "mod.bat" according to the instructions, I tried to launch the program with either the "mod" or modeller6v2" command from "C:\modeller6v2\bin\" directory. The result was the following: *************************************************************************** Microsoft Windows 2000 [Versión 5.00.2195] (C) Copyright 1985-2000 Microsoft Corp. C:\>cd modeller6v2 C:\modeller6v2>cd bin C:\modeller6v2\bin>mod C:\modeller6v2\bin>set MODINSTALL6v2=c:\modeller6v2 C:\modeller6v2\bin>set KEY_MODELLER6v2=XXX C:\modeller6v2\bin>set LIBS_LIB6v2=c:\modeller6v2\modlib\libs.lib C:\modeller6v2\bin>set EXECUTABLE_TYPE6v2=i386-windf C:\modeller6v2\bin>set PATH=C:\WINNT\system32;C:\WINNT;C:\WINNT\System32\Wbem;c:\modeller6v2\bin C:\modeller6v2\bin>c:\modeller6v2\bin\modeller6v2 MODELLER 6v2, 17 Feb 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, Windows_NT AARRLUQ x86 Family 6 Model 8 Stepping 6, GenuineI Date and time of compilation : Jul 09 2002 16:21:30 Job starting time (YY/MM/DD HH:MM:SS): 2003/07/30 11:02:40.776 fullfn__230E> File not found: mod Directories: :${MODINSTALL6v2}/bin/ Extensions : .top: Prefixes : nothing, pdb recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 2190959 2139. 608 2.089 Starting time : 2003/07/30 11:02:40. 776 Closing time : 2003/07/30 11:02:43. 000 Total CPU time [seconds] : 1.85 C:\modeller6v2\bin> This is exactly the same error I've previously got with the Linux version. I don't know if I'm forgetting something in the line of commands. Thank you very much for your assistance, and sorry for such a naïve question. Sincerely yours, Antonio Arroyo

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FW: modeling problem
by Modeller Care 29 Jul '03

29 Jul '03

------ Forwarded Message From: Feng Cui <fengcui(a)iastate.edu> Date: Tue, 29 Jul 2003 21:28:31 -0500 (CDT) To: modeller-care(a)salilab.org Subject: modeling problem Sir, I am doing a project on homology modeling using Modeller. My question is following: The target sequence has 5 domains (519aa in total). I can find a template structure for the first two domains (Part I), and another template structure for the last three domains (Part II). Part I and Part II are separated by a gap with 7 amino acids in length. fortunately i found a piece of peptide (9 aa) which can fill the gap (in 7/9 indentity) and anchored on the Part I and II. can i made a model based on the "contig" piece by piece? should i trust the model, e.g. the relative orientation of Part I and Part II? have you met a similar problem? any suggestion would be appreciated. or you may forward the message to the discussion forum. thank you very much for your help. Feng Cui ------ End of Forwarded Message

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building a model with water molecules.
by Moshe Amitay 27 Jul '03

27 Jul '03

Hi to all: About modeling with water - I tried to model a protein with water molecules that exist in the PDB file. I wrote in my TOP file: "SET HYDROGEN_IO = off, HETATM_IO = off, WATER_IO = on", replaced the word 'HETATM' with 'ATOM' in th PDB file and add to the end of the alignment, "/wwwww*" (5 molecules). But, Modeller didn't recognize the water molecules in the PDB file. the error notification was: "Number of residues in the alignment and pdb files are different: 345 340 For alignment entry: 2 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 - the template sequance is 340 aa, and I add 5 water molecules. The PDB file containes 340 aa and 5 water molcules. Could someone explaine me how to overcome this problem ? thanks a lot for your help. Moshe. --------------------------------------------------------------------- Moshe Amitay, Bilha Fischer's lab Dept. of Chemistry Bar-Ilan University ISRAEL.

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Distance restraints cause segmentation faults
by Modeller Care 25 Jul '03

25 Jul '03

------ Forwarded Message From: owner-modeller_usage(a)salilab.org Date: Fri, 25 Jul 2003 09:31:27 -0700 To: modeller_usage-approval(a)salilab.org Subject: BOUNCE modeller_usage(a)salilab.org: Non-member submission from ["Thorsten Schweikardt" <thorsten(a)mail.uni-mainz.de>] Dear all, I am having a problem with the add_restraints-command: using Modeller6v2 (linux/windows-version), I am trying to model the N-terminus of a protein using experimental distance-data. The rest of the protein is available as pdb-file and serves as template for the C-terminal end. Using the linux-version does not work well: without implementing the distances or when implementing only the _first_ distance (see below), modeller works fine, but as soon as I want to use another or more than this first distance, modeller crashes with a segmentation fault. Using the windows-version with the script below, models are produced that have an n-terminus formed like a straight line, as if the distance restraints that were meant to guide the structure are simply ignored or not read in... I tried to change the corresponding atoms from 'OG' to 'CA' in case this option only works with certain atom types, but this had no effect. Can someone tell me what I am doing wrong? Many thanks in advance, Thorsten Schweikardt Molecular Biophysics University of Mainz Top-File: ----------------------------- INCLUDE SET ALNFILE = 'alignment.ali' SET KNOWNS = 'protein1' SET SEQUENCE = 'protein1plusnterm' SET ATOM_FILES_DIRECTORY = './' SET STARTING_MODEL= 1 SET ENDING_MODEL = 20 SET LIBRARY_SCHEDULE = 4 SET FINAL_MALIGN3D = 1 CALL ROUTINE = 'model' SUBROUTINE ROUTINE = 'special_restraints' SET ATOM_IDS = 'OG:3' 'OG:169' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 30.0 10.0 SET ATOM_IDS = 'OG:116' 'OG:169' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 40.0 0.0 SET ATOM_IDS = 'CA:42' 'CA:169' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 40.0 1.0 SET ATOM_IDS = 'CA:3' 'CA:42' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 21.0 4.0 SET ATOM_IDS = 'CA:3' 'CA:116' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 50.0 1.0 RETURN END_SUBROUTINE ------ End of Forwarded Message

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upper residue number modeling limit?
by Timothy Minh 25 Jul '03

25 Jul '03

Hello Modeller users, I was wondering if there was a limit in the amount of residues that MODELLER 6v2 can take. I have been able to model proteins approx 250 in length, but I've not been able to model larger proteins of approx 1300 residues. I would appreciate any suggestions/comments that you may have. Thank you! Tim Minh

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Do residue topology entries for nucleotides exist?
by Andy Torelli 24 Jul '03

24 Jul '03

Dear MODELLER Users, I would like to contact anyone who has created or obtained the necessary residue entries (in residue topology file format) that, when added to the top_heav.lib library, enable modeling nucleotides. The copy of top_heav.lib that I have does not have all the nucleotides. I am interested in both the RNA and DNA forms of these molecules. I have looked into creating these entries on my own, but it will take me some time to obtain the software to do so. If anyone has these library entries already, it would save a lot of time. Thank you for your time, Sincerely, -Andy Torelli Ph.D. Student, University of Rochester, Department of Biochemistry and Biophysics

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Creating an oligonucleotide sequence.
by Andy Torelli 18 Jul '03

18 Jul '03

Dear MODELLER Users, I would like to model a short nucleotide sequence as a substrate for an enzyme. In the top_heav.lib file, I notice that the listing for URA (a uridine mono-phosphate molecule) has bond angle entries that include '+' and '-' prefixes on some of the atoms (referring to atoms in molecules adjacent in a chain sequence). I was under the impression that these entries were enough to form a connected sequence of molecules (in this case, an oligonucleotide). In my alignment file, I have two of these URA molecules situated next to each other (separated from the amino acids of my enzyme by a chain break character '/'), but in the final model, they do not appear to be bonded to each other. As a test, I substituted two amino acids for the two URA molecules and noticed that in the final model, they were not joined by a bond either. Since the amino acids of my enzyme were all clearly bonded to each other, this result made me wonder if MODELLER was not recognizing my two substrate molecules as being members of a chain themselves (albeit two subunits long). - Do I need to, or can I, explicitly define these two (nucleotide) molecules as being members of a chain such that MODELLER will create a phosphodiester bond between them? - Is it possible that they would normally be bonded, but during the simulation, the molecules are being "torn apart"? - My other option appears to be to impose a "special_patches" restraint (that I would have to add to the top_heav.lib file) to explicitly join them. However, seeing that the URA residue listing already appears to be set up for nucleotide chains, this seems like it would be unnecessary. Thanks for your time, Sincerely, -Andy Torelli Ph.D. Student University of Rochester, Department of Biochemistry and Biophysics

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mod6v2 still doesn't work on FreeBSD
by Peter C. Lai 17 Jul '03

17 Jul '03

Hi everyone, I asked about using modeller 6v2 last year on FreeBSD which did not work. After redownloading the latest build from Bozidar, running mod6v2-i386-absoft on FreeBSD results in computation of stuff but no files are output, and around the time the modelling should be complete, it core dumps with Bad system call. This happens with running mod6v2-i386-nag also. I know Nag has a port of the F95 compiler for FreeBSD; not sure if you guys have a copy or not. Currently, I'm using modeller on my windows machine, but it would really be nice to run it on my FreeBSD workstation. In the previous year I have been running it on SGI, but currently the SGI is being used for dynamics. My FreeBSD setup is 4.8-STABLE, with linux_base-7.1 (linux emulation ABI) installed. Wondering if you had any suggestions. Thanks. pete -- Peter C. Lai University of Connecticut Dept. of Molecular and Cell Biology Yale University School of Medicine SenseLab | Research Assistant http://cowbert.2y.net/

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