July 2002 - modeller_usage

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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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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RTF file for HYP
by Lesheng Kong 30 Jul '02

30 Jul '02

Hi, I have made an all-hydrogen topology file for HYP(4-hydroxyproline). BUT How MODELLER's non-hydrogen topology and other topologies was derived? I attach my RTF file for HYP as follows: MASS 30 N 14.00700 N MASS 20 CP1 12.01100 C MASS 6 HB 1.00800 H MASS 23 CC 12.01100 C MASS 44 O 15.99900 O MASS 21 CP2 12.01100 C MASS 3 HA 1.00800 H MASS 13 CT1 12.01100 C MASS 47 OH1 15.99900 O MASS 1 H 1.00800 H MASS 22 CP3 12.01100 C MASS 15 CT3 12.01100 C MASS 11 C 12.01100 C MASS 35 NH2 14.00700 N DECL -N DECL +C AUTO ANGLES DIHE RESI HYP 0.00000 GROUP ! HD1 HD2 ATOM N N -0.2900 ! | \ / ATOM CA CP1 0.0200 ! N---CD HG ATOM HA HB 0.0900 ! | \ / GROUP ! | CG ATOM C CC 0.5300 ! | / \ ATOM O O -0.5300 ! HA-CA--CB OG2--HG2 GROUP ! | / \ ATOM CB CP2 -0.1800 ! | HB1 HB2 ATOM HB1 HA 0.0900 ! O=C ATOM HB2 HA 0.0900 ! | GROUP ATOM CG CT1 0.1400 ATOM HG HA 0.0900 ATOM OG2 OH1 -0.6600 ATOM HG2 H 0.4300 GROUP ATOM CD CP3 0.1800 ATOM HD1 HB 0.0000 ATOM HD2 HB 0.0000 BOND N CA N CD CA HA CA CB CA C BOND C O CB HB1 CB HB2 CB CG CG HG BOND CG OG2 CG CD CD HD1 CD HD2 N +C BOND C N OG2 HG2 IMPH N CA CD +C C CA N O DONOR HG2 OG2 ACCEPTOR O C IC CD N CA CB 1.4468 114.9587 -11.2918 101.8808 1.5360 IC CD N CA HA 1.4468 114.9587 -129.2290 110.5162 1.0924 IC CD N CA C 1.4468 114.9587 109.5875 111.6376 1.5380 IC HA CA N +C 1.0924 110.5162 50.0429 122.5076 1.3162 IC CD +C *N CA 1.4468 122.5296 -179.2170 122.5076 1.4550 IC CA N CD CG 1.4550 114.9587 -11.8599 102.4794 1.5305 IC CA N CD HD1 1.4550 114.9587 -131.8901 111.1069 1.0924 IC CA N CD HD2 1.4550 114.9587 106.0401 109.5406 1.0925 IC N CA CB CG 1.4550 101.8808 29.6080 103.6605 1.5362 IC N CA CB HB1 1.4550 101.8808 152.0681 112.9350 1.0925 IC N CA CB HB2 1.4550 101.8808 -86.5729 108.9663 1.0930 IC N CA C O 1.4550 111.6376 149.4002 120.4223 1.2316 IC N CA C N 1.4550 111.6376 -31.0428 120.0469 1.3161 IC N CA *C O 1.3161 120.0469 -179.5571 120.4223 1.2316 IC CA CB CG OG2 1.5360 103.6605 -158.7449 112.5784 1.4300 IC CA CB CG HG 1.5360 103.6605 79.0616 109.5554 1.0926 IC CD CG OG2 HG2 1.5305 112.2089 31.3937 109.5000 1.0300 IC N CD CG CB 1.4468 102.4794 29.9288 103.3139 1.5362 PATC FIRS PROP LAST CTER Any comment or suggestion for it? Thank you very much! With best regards, Kong Lesheng

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Chains A,B,C,D
by Frederico Moreno 29 Jul '02

29 Jul '02

Hi, Please, I'm trying to use a tetrameric protein template, but I'm getting some trouble. The pdb file show the chains A, B, C and D atoms positions. So what do I have to change in my alingment an TOP files to run modeller correctly? Frederico Moreno _______________________________________________________________________ Yahoo! PageBuilder O super editor para criação de sites: é grátis, fácil e rápido. http://br.geocities.yahoo.com/v/pb.html

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MPAIRS
by Cameron Long 29 Jul '02

29 Jul '02

When running a two domain target modeling job an error message in the log file said that the MPAIRS array was too small. What is the MPAIRS array, and how do I avoind this problem? Cameron Long

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hetero atoms
by Cameron Long 29 Jul '02

29 Jul '02

How are hetero atoms read from pdb files and included in the modeling target?

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Mac OS X MODELLER 6v2 is here!
by Bozidar Yerkovich 26 Jul '02

26 Jul '02

Hi all, As you have probably found out already, I just put up on the web Apple OS X version of MODELLER 6v2, for those of you who wanted this executable, and for those of you who consider switching to Mac ;-) It's compiled on OS X 10.1.5, using absoft f95 v7.0a. It gets installed as any other UNIX executable, so just run Install script, and follow the questions. I also improved the script a little, so it finds if you already have/had MODELLER installed on your machine before, which means you have to do almost no typing, in most cases, only hitting "Return". But please remember to 'source ~/.cshrc' Best, Bozidar

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