modeller_usage August 2002

modeller_usage@salilab.org

14 participants
22 discussions

SS bridges
by Bozidar Yerkovich 14 Aug '02

14 Aug '02

>From Eric: Hi Pedro; You can tell modeller to make particular disulfide bridges using this sub routine: SUBROUTINE ROUTINE = 'special_patches' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '160: ' '190: ' # 160 is the cystein number on the sequence PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '122: ' '206: ' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '76: ' '128: ' RETURN END_SUBROUTINE Good luck Eric ------------------------------------ Dr Eric Feyfant Computational Chemist Departement of Biological Chemistry Wyeth Research 85 Bolton St. Cambridge, MA 02140 tel: +1 617 665 8987 fax: +1 617 665 8993 email: efeyfant(a)wyeth.com

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disulfide bridges
by Pedro A Reche 14 Aug '02

14 Aug '02

Hi all, I am modelling a protein that should have 3 disulfide bridges however the model I am getting does not shown them. Does any know how to tell modeller the cys pairs that are making disulfide bridges? Cheers, Pedro ******************************************************************* PEDRO A. RECHE , pHD TL: 617 632 3824 Dana-Farber Cancer Institute, FX: 617 632 4569 Harvard Medical School, EM: reche(a)research.dfci.harvard.edu 44 Binney Street, D1510A, EM: reche(a)mifoundation.org Boston, MA 02115 URL: http://www.reche.org *******************************************************************

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problems with optimaze
by Pedro A Reche 14 Aug '02

14 Aug '02

Hi all, I am trying to optimaze a model by just running the follwing script: Example for: OPTIMIZE, SWITCH_TRACE # This will optimize stereochemistry of a given model, including # non-bonded contacts. READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib' READ_PARAMETERS FILE = '$(LIB)/par.lib' READ_MODEL FILE = '1c11' SEQUENCE_TO_ALI ATOM_FILES = '1c11', ALIGN_CODES = '1c11' SEQUENCE_TO_ALI ADD_SEQUENCE = on, ATOM_FILES = ATOM_FILES '1c11.ini', ; ALIGN_CODES = ALIGN_CODES '1c11-ini' GENERATE_TOPOLOGY SEQUENCE = '1c11-ini' TRANSFER_XYZ BUILD_MODEL INITIALIZE_XYZ = off WRITE_MODEL FILE = '1c11.ini' # Generate the restraints: MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo' WRITE_RESTRAINTS FILE = '1c11.rsr' ENERGY DYNAMIC_SPHERE = on SWITCH_TRACE TRACE_OUTPUT = 1, FILE = '1c11.trc' OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 20 OPTIMIZE OPTIMIZATION_METHOD = 3, TEMPERATURE = 300, MAX_ITERATIONS = 50 OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 20 ENERGY WRITE_MODEL FILE = '1c11.B' Unfortunally, I am getting the an error after running mod optimaze.top, and I do not see what is wrong, possble something silly but I do not wee where the problem is. So any help will be very welcomed. 1c11 is the name of the model. I moved Here it follows the optimaze.log 1c11.B99990001 to 1c11. 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 mif.dfci.harvard.edu 2.4.13 i686 Date and time of compilation : 05/24/2002 09:27:23 Job starting time (YY/MM/DD HH:MM:SS): 2002/08/13 12:19:52.681 rdactio_534E> Command not recognized: EXAMPLE FOR: OPTIMIZE, SWITCH_TRACE recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 2190959 2139.608 2.089 Starting time : 2002/08/13 12:19:52.681 Closing time : 2002/08/13 12:19:54.367 Total CPU time [seconds] : 1.58 -- ******************************************************************* PEDRO A. RECHE , pHD TL: 617 632 3824 Dana-Farber Cancer Institute, FX: 617 632 4569 Harvard Medical School, EM: reche(a)research.dfci.harvard.edu 44 Binney Street, D1510A, EM: reche(a)mifoundation.org Boston, MA 02115 URL: http://www.reche.org *******************************************************************

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Error message
by Troy Wymore 13 Aug '02

13 Aug '02

Hello Modellers! I have an error message popping up and am not sure how to interpret. Here it is: delete__443_> Restraints marked for deletion were removed. Total number of restraints before, now: 41972 38728 act10___551E> No such routine: recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 I have not updated my Modeller6 to Modeller6v2 yet. Maybe that's the problem. Any help is much appreciated. Troy Wymore Pittsburgh Supercomputing Center Biomedical Initiative Group

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Admin update: modeller_usage digest
by Bozidar Yerkovich 12 Aug '02

12 Aug '02

Hi everybody, Over the last couple of weeks, I noticed increase in number of people subscribing to digested version of the list. To make it easy for them and others browsing archives, I'd ask all of us to clean up our replies a little bit, before we send them. For example, we should remove our signature lines/files, remove lines of original question that include greetings/good-byes, rewrap paragraphs, etc. Thanks for your help in making this list safe, easy-tu-use and informative for all of MODELLER users. Happy modeling, Bozidar

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"Array too small. Increase MBNDPF"
by Kong Lesheng 12 Aug '02

12 Aug '02

Dear Dr. Bozidar Yerkovich, I have added topology of HYP into top.lib, and modified restyp.lib(using "o" as residue code for HYP). But when I did modelling, it reported the following errors and warnings. addprm__223E> Array too small. Increase MBNDPF recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 getf_______W> RTF restraint not found in the atoms list: getf_______W> RTF restraint not found in the atoms list: getf_______W> RTF restraint not found in the atoms list: iatmcls_286W> MODEL atom not classified: ALA:OT1 ALA iatmcls_286W> MODEL atom not classified: ALA:OT2 ALA r_stere_607W> Cannot find params in params file: addprm__440W> Adding params (mean,force,period): 1.5431 300.0000 1 r_stere_607W> Cannot find params in params file: addprm__440W> Adding params (mean,force,period): 3.0698 300.0000 1 r_stere_607W> Cannot find params in params file: addprm__440W> Adding params (mean,force,period): 1.0924 300.0000 1 r_stere_607W> Cannot find params in params file: addprm__440W> Adding params (mean,force,period): 3.8828 300.0000 1 r_stere_607W> Cannot find params in params file: addprm__440W> Adding params (mean,force,period): 66.6866 60.0000 1 r_stere_607W> Cannot find params in params file: addprm__440W> Adding params (mean,force,period): 111.1069 60.0000 1 ....... How could I fix these problem? I attach an uuencoded compressed tar archive of all input and output files. Thank you very much! With best regards, Kong Lesheng --------------------------------- BioInformatics Center National University of Singapore 10 Kent Ridge Cresent Singapore119260 Tel: (65)6874 4459 Fax: (65)6778 2466 ---------------------------------

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Re: Modeller6v2 installation problem
by Bozidar Yerkovich 06 Aug '02

06 Aug '02

Huw, Make sure that user huw has admin privileges. Also run it under 10.1.5., because that's where I tested the script. Other then that I have no idea what's could be wrong. Everything seems fine to me. Good luck, Bozidar > Bozidar, > > Here is the logfile on trying to run your Modeller6v2 install script on > a Mac OSX machine. It does not seem to work. I expect I am doing > something _really_ stupid, but any thoughts you have as to what is going > wrong would be much appreciated. Thanks! > > Huw > > PS I'm certain I ran it under tcsh > > logfile follows (sorry if it gets garbled) : > > ________________________________ > > [besserm5:~] huw% cd desktop/modeller6v2 > [besserm5:~/desktop/modeller6v2] huw% ./Install > > > > Installation of MODELLER6v2 > > This script will install MODELLER6v2 into a specified directory for > which you have read/write permissions. It will also install the current > user as a MODELLER6v2 user. To allow other users running MODELLER6v2, > you need to follow instructions at the end of this script or in the > INSTALLATION file. > > This installation will modify your login script, but only after you > agree to it explicitly. The original login script will be backed up. > > Your login shell needs to be csh, tcsh or a compatible shell. > > You can generally find your current shell by typing 'echo $shell'. > > If your login shell is not csh compatible, exit now (ctrl-c), edit the > scripts/logscript.template file to comply with your shell or change your > login shell to csh or tcsh, and then run this installation script again. > > To accept the default answers indicated in [...], press <Enter> only. > > ------------------------------------------------------------------------ > > The currently supported architectures are as follows: > > 1) Linux PC (e.g. RedHat, SuSe). > 2) SUN Inc. Solaris workstation. > 3) Silicon Graphics Inc. IRIX workstation. > 4) DEC Inc. Alpha OSF/1 workstation. > 5) Linux PC (Mandrake). > 6) IBM AIX OS. > 7) Apple Mac OS X. > > Select the type of your computer from the list above [1]: 7 > > Full directory name for the installed MODELLER6v2 > [/Users/huw/bin/modeller6v2]: > There is no such directory; it will be created. > > Full file name of your login script [/Users/huw/.cshrc]: > There is no such file; it will be created. > > KEY_MODELLER6v2, obtained from our academic license server at > http://salilab.org/modeller/registration.shtml: > > ------------------------------------------------------------------------ > > The following settings will be used: > > The type of this machine : 7 > Destination installation directory: /Users/huw/bin/modeller6v2 > The name of the login script : /Users/huw/.cshrc > KEY_MODELLER6v2 : > > If they are incorrect, abort installation (ctrl-c) and run Install > again. No changes to your system have been made yet. Installation > involves: > > 1. The destination installation directory will be deleted and then > created from scratch. > > 2. The login script will be backed up and then modified. > > Press <Enter> to begin the installation: > > ------------------------------------------------------------------------ > > Running make install ... ./Install: command not found: make [143] > > ------------------------------------------------------------------------ > > Editing the login script /Users/huw/.cshrc ... find: > /Users/huw/bin/modeller6v2: No such file or directory find: > /Users/huw/bin/modeller6v2: No such file or directory > > ------------------------------------------------------------------------ > > If you have problems with installation, please see the INSTALLATION > file. > > MODELLER6v2 documentation in the PDF and HTML formats can be found in > the /Users/huw/bin/modeller6v2/doc directory. > > A simple homology modeling test case is in examples/tutorial-model/. > > To complete instalation of MODELLER6v2, please type now source > /Users/huw/.cshrc > > To allow other users on this system to use MODELLER6v2, please include > the following lines into their login script: > > ### begin MODELLER6v2 > ###################################################### > > setenv MODINSTALL6v2 /Users/huw/bin/modeller6v2 > setenv EXECUTABLE_TYPE6v2 macx-absoft > setenv LIBS_LIB6v2 $MODINSTALL6v2/modlib/libs.lib > setenv KEY_MODELLER6v2 XXX > alias mod mod6v2 set path=($path $MODINSTALL6v2/bin) > limit stacksize unlimited > > ### end MODELLER6v2 > ######################################################## > > ------------------------------------------------------------------------ > > Happy modeling! MODELLER Team, 2002 > -- "...when you look long into an abyss, the abyss also looks into you." Friedrich Nietzsche http://www.stormloader.com/photo

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OSF versions of 6v0 and 6v2 give illegal instruction error
by Robert Williams 04 Aug '02

04 Aug '02

The 6v0 and 6v2 versions of modeller for Digital Unix (OSF) yield an "Illegal instruction - core dumped" message on all of my OSF machines at various version levels (V4.0F for example). Earlier versions of modeller worked on these machines. Has anyone else seen this? Is there a fix? Bob Williams

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Re: Error message
by Bozidar Yerkovich 02 Aug '02

02 Aug '02

Troy, Yes, it's refine_x, where x is 1-5. 1 is quick and 5 is slow MD annealing. 3 works fine for me, most of the time. I hope this helps... Bozidar > Hello Bozidar, > > I have nailed down the problem with the error. It seems that if I comment > out the part of > SET MD_LEVEL = 'refine1' > > then it works. Also if I have it as > > SET MD_LEVEL = 'nothing' ; then it works. > > Still I need to find out what does work as far as MD annealing. > > Take your time answering back. I know how it is to be swamped. > > Take care, > > Troy > > -- "My riches consist not in the extent of my possessions, but in the fewness of my wants." - J. Brotherton

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Re: modeller restrain
by Bozidar Yerkovich 02 Aug '02

02 Aug '02

Hi all, It seems that we may have a bug in beta sheet restrain option. If you are certain that you have this problem, can you please send me your tar-ball, so that I can reproduce the error here. Thanks, Bozidar > amit luthra wrote: >> >> sir, >> Thanks for reply >> I have already used this programme but the portion is >> not restaining in particular conformation. >> amit luthra >> >> ________________________________________________________________________ >> Want to sell your car? advertise on Yahoo Autos Classifieds. It's Free!! >> visit http://in.autos.yahoo.com > > Maybe there is a bug in the program. It would be useful if you send an > example and explanation to bozidar(a)salilab.org > illustrating this problem, > Thank you, > > Andras > -- To handle yourself, use your head, To handle others, use your heart.

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modeller_usage August 2002