- modeller_usage - salilab.org

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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CHARMM version?
by Dinesh Soares 01 Aug '02

01 Aug '02

Hi, What version of CHARMM do you use with your latest MODELLER 6v2? Many thanks, Dinesh (PhD student - University of Edinburgh) <html></html> _________________________________________________________________ Join the worlds largest e-mail service with MSN Hotmail. http://www.hotmail.com

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MAXRER
by Alessandro Contini 01 Aug '02

01 Aug '02

I'm try to compare different structures found by a seqsearch.top script with a compare.top script based on the compare.top present in one of the tutorials, but I get an error that look like this: pntdp___E> Increase MAXRES or gap penalities. Wat does MAXRES do and how can I eventually increase it? Thank you all Alessandro -- Dott. Alessandro Contini Istituto di Chimica Organica, Facoltà di Farmacia Università degli Studi di Milano Via Venezian, 21 20133 Milano Tel. +390250314480 Fax +390250314476 http://users.unimi.it/istchimorg/pagconthtm.htm

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How much time?
by Shamshad Zarina 31 Jul '02

31 Jul '02

Dear All, I have a strange question. How fast is Win-modeller as compared to linux version? Ofcourse that would depend on individual system as well, but I have a feeling that Windows version is slower than linux. I tried to model a protein having 480 amino acids and even after three hours, Win-modeller6 was still running. Is is normal or there is something wrong? thanks in advance, Sincerely, Shamshad __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.yahoo.com

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Why MODERLLER6v2 cannot recognize these Variables?
by Lesheng Kong 30 Jul '02

30 Jul '02

Hi, When do modeling, I got the following error message: assgn___544E> Variable name not recognized: MODEL_TOPOLOGY Command line: SET MODEL_TOPOLOGY = 1, HYDROGEN_IO = ON, HETATM_IO =ON, WATER_IO = ON assgn___525E> Error in TOP variable assignment. assgn___544E> Variable name not recognized: TOPOLOGY_LIBRARY Command line: SET TOPOLOGY_LIBRARY = $(LIB)/TOP.LIB assgn___525E> Error in TOP variable assignment. assgn___544E> Variable name not recognized: PARAMETERS_LIBRARY Command line: SET PARAMETERS_LIBRARY = $(LIB)/PAR.LIB assgn___525E> Error in TOP variable assignment. compile_563E> Please correct the errors reported above and rerun MODELLER. recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 But I follow FAQ 15, why MODERLLER6v2 cannot recognize these Variables? Is it possible that my installation has problems? Thank you very much! Kong Lesheng My model.top: INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 SET ALNFILE = '1TCH-1TCG.ali' SET KNOWNS = '1TCH' SET SEQUENCE = '1TCG' SET ATOM_FILES_DIRECTORY = './:../atom_files' SET STARTING_MODEL = 1 SET ENDING_MODEL = 5 SET MODEL_TOPOLOGY = 1, HYDROGEN_IO = ON, HETATM_IO=ON, WATER_IO = ON SET TOPOLOGY_LIBRARY = $(LIB)/top.lib SET PARAMETERS_LIBRARY = $(LIB)/par.lib CALL ROUTINE = 'model'

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