- modeller_usage - salilab.org

modeller error
by rathankar rao 07 Mar '05

07 Mar '05

Dear sir i have just started using modeller7v7 but have landed in to some problems.i have a few doubts 1. which directory should i place the top files, ali files and the pdb files. i placed top files in the bin, pdb files in atom-files directory. and tried to run the command, but it shows this error MODELLER 7v7, Sep 12, 2004 09:15pm PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2004 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom, N. Eswar, F. Alber, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA 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, Win2000 build 2195 Service Pack 4, PROJECTBT, uni, x86 Family 15 Model 2 Stepping 9 Date and time of compilation : 09/13/2004 17:17:22 Job starting time (YY/MM/DD HH:MM:SS): 2004/12/27 13:26:51.093 TOP_________> 109 749 SET ALNFILE = 'seqalin.ali' TOP_________> 110 750 SET KNOWNS = '1ocs' TOP_________> 111 751 SET SEQUENCE = 'yhr' TOP_________> 112 752 SET ATOM_FILES_DIRECTORY = './:../atom_files' TOP_________> 113 753 SET STARTING_MODEL = 1 TOP_________> 114 754 SET ENDING_MODEL = 1 TOP_________> 115 755 CALL ROUTINE = 'model' TOP_________> 116 419 CALL ROUTINE = 'getnames' TOP_________> 117 534 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL' TOP_________> 118 535 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; ' TOP_________> 119 536 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE TOP_________> 120 537 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE TOP_________> 121 538 SET ROOT_NAME = SEQUENCE TOP_________> 122 539 RETURN TOP_________> 123 420 CALL ROUTINE = 'homcsr' TOP_________> 124 112 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE Dynamically allocated memory at amaxseq [B,kB,MB]: 84067 82.097 0.080 fullfn__230E> File not found: seqalin.ali Directories: Extensions : :.ali Prefixes : nothing, pdb recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 84067 82.097 0.080 Starting time : 2004/12/27 13:26:51.093 Closing time : 2004/12/27 13:26:52.078 Total CPU time [seconds] : 0.97 --------------------------------- Celebrate Yahoo!'s 10th Birthday! Yahoo! Netrospective: 100 Moments of the Web

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bug report
by prakesh amresh 06 Mar '05

06 Mar '05

Dear administrator, Doing working on modeller7v7 at window workstation some command is not working Eg; C:\modeller>call routine = model Gives massage routine is not recognized as an internal or external command, operable program or batch file. Similar problem occur with read topology Plz , guide me through mail. Tks.

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docking software
by Tong Chen 03 Mar '05

03 Mar '05

Hi! All: I need do some docking studies. It would be greatly appreciated if anyone can recommend some good free softwares. Thanks a lot Tong Tong Chen School of Biological Sciences Flinders University GPO Box 2100 Adelaide 5001 Email: Tong.Chen(a)flinders.edu.au Phone: (08) 8201-3836

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new to modeller - optimization of homology model
by Scavetta, Robert D. 01 Mar '05

01 Mar '05

Hi all, I am new to MODELLER and require some assistance. I have generated a homology model of the NDB heterodimer of a ABC protein, containing 2 ATP molecules and 2 Mg+2 ions. The homology model requires optimization. Please advise. Robert Robert D. Scavetta, PhD Special Projects Associate Mayo Clinic College of Medicine Department of Biochemistry and Molecular Biology 13400 E. Shea Boulevard Scottsdale, AZ 85259 (480) 301-6963 phone (480) 301-7017 fax Scavetta.Robert(a)Mayo.Edu

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Optimization or Refinement of Homology Model
by David Piper 22 Feb '05

22 Feb '05

Modellers, 1) What level of refinement or MD_LEVEL is used as a default? My top script is like this: # A sample TOP file for fully automated comparative modeling INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 2 SET ATOM_FILES_DIRECTORY = '/mod6v2/ATOMS'SET ALIGNMENT_FORMAT = 'PIR' SET ALNFILE = 'model.ali' SET KNOWNS = 'template' SET SEQUENCE = 'model' SET STARTING_MODEL=1 SET ENDING_MODEL=10 CALL ROUTINE = 'model' SUBROUTINE ROUTINE = 'special_restraints' ##there are a number of alpha helical and symmetry restraints ##omitted here for clarity. RETURN END_SUBROUTINE 2) After modelling, if there are "bumps" or poorly defined bond lengths or angles (based on ProCheck output), what is the preferred way of optimizing them? Thanks for any input, David

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(no subject)
by Mensur Dlakic 21 Feb '05

21 Feb '05

Hi all, Can someone provide an explanation about converting Modeller's dihedral restraints into plain psi/phi/omega angles? I have read through the manual and have an intuitive feel for the way Modeller calculates these values, but there are so many columns in the output file that I still am not able to decipher it. So my question is is what columns in the restraint file correspond to dihedral angles and their deviations, and how do I convert them back to numbers in the -180 to 180 range. Thanks for your help, Mensur ========================================================================== | Mensur Dlakic, PhD | Tel: (406) 994-6576 | | Department of Microbiology | Fax: (406) 994-4926 | | Montana State University | | | 109 Lewis Hall, P.O. Box 173520 | http://myprofile.cos.com/mensur | | Bozeman, MT 59717-3520 | E-mail: mdlakic(a)montana.edu | ==========================================================================

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protein-ligand complex
by Praveen Madala 21 Feb '05

21 Feb '05

Hi Modellers, I would like to know, Is there anyway to modell a protein-ligand complex by modeller??????? If there is one, can you please tell me where can I get the information. Thanking you......... regards, Praveen On Mon, 21 Feb 2005 14:41:21 -0800 modeller_usage-request(a)salilab.org wrote: > Send modeller_usage mailing list submissions to > modeller_usage(a)salilab.org > > To subscribe or unsubscribe via the World Wide Web, >visit > http://salilab.org/mailman/listinfo/modeller_usage > or, via email, send a message with subject or body >'help' to > modeller_usage-request(a)salilab.org > > You can reach the person managing the list at > modeller_usage-owner(a)salilab.org > > When replying, please edit your Subject line so it is >more specific > than "Re: Contents of modeller_usage digest..." > > > Today's Topics: > > 1. setting the DEVIATION (Ori Kalid) > 2. Atom Index is out of bounds: (Amjad Farooq) > 3. Re: setting the DEVIATION (Karsten Suhre) > 4. Regarding modelling (rajesh rengaraj) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 20 Feb 2005 16:18:35 +0200 >From: "Ori Kalid" <kalido(a)mail.biu.ac.il> > Subject: [modeller_usage] setting the DEVIATION > To: <modeller_usage(a)salilab.org> > Message-ID: <00f801c51757$176c6320$551b4684@W2000EPRO> > Content-Type: text/plain; charset="windows-1255" > > Hi Everyone, > > Does anyone know how to control the XYZ randomization >parameter DEVIATION? > I tried modifying its value using a simple SET DEVIATION >= 0.0, but nothing happens. The reasults are the same as >for the default value of 4.0. > > Thanks, > > Ori > >

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Atom Index is out of bounds:
by Amjad Farooq 21 Feb '05

21 Feb '05

Dear Modeller users, I am trying to model the structure of a 300-residue protein containing a phospho-threonine (PTH). After writing the topology of PTH in top_heavy.lib and specifying PTH in restype.lib under the modlib subdirectory, I get this error upon running MODELLER: csrrng__299E> Atom index is out of bounds: 2392 2391 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 As you can see MODELLER does not complain about PTH but some general error. Has anyone encountered something like this before? How can this be fixed? Interestingly, when I substitute PTH with THR, MODELLER generates no such error and models the structure nicely. Any help will be greatly appreciated. Many thanks, Amjad **************************************** AMJAD FAROOQ PhD Assistant Professor Dept of Biochemistry & Molecular Biology Miller School of Medicine University of Miami Gautier Building, Rm 214 1011 NW 15th Street Miami, FL 33136 tel 305-243-2429 fax 305-243-3955 amjad(a)farooqlab.ws http://farooqlab.ws ****************************************

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Regarding modelling
by rajesh rengaraj 21 Feb '05

21 Feb '05

Hello modellers, Is it possible to model 1249 amino acids at a stretch by using modeller, where the target sequence is having less similarty with the template. I found the template by using the fold recognition method. Please help me modellers. --------------------------------- Do you Yahoo!? Yahoo! Search presents - Jib Jab's 'Second Term'

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setting the DEVIATION
by Ori Kalid 21 Feb '05

21 Feb '05

Hi Everyone, Does anyone know how to control the XYZ randomization parameter DEVIATION? I tried modifying its value using a simple SET DEVIATION = 0.0, but nothing happens. The reasults are the same as for the default value of 4.0. Thanks, Ori

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