March 2005 - modeller_usage

amino acid numbering
by Michael Grabe 11 Mar '05

11 Mar '05

Hello all, i make models that have multiple chains, and i would like the models to have amino acid numbers that don't start at 1, and that are not continuous from the end of chain i to the beginning of chain i+1. can some one send a sample alignment file that does this? thanks, michael ------------------------------------------------------------------------ -------------------------- Michael Grabe, Ph.D. HHMI/UCSF Genetics Development & Behavioral Science Building 1550 4th Street, GD 481 San Francisco, CA 94143-0725 tel: ++ 415.476.0421 http://itsa.ucsf.edu/~mgrabe

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help
by arul prakasam peter 11 Mar '05

11 Mar '05

sir my name is arul and doing molecular modeling using modeller.sir iam modeling two proteins one of my target protein has 35% similarity and other have 55% similarity with their respective templates.sir for running the modeller as i have to give three input files namely script file ,pdb file,alignment file. sir my questions are 1.if if want to create my own alignment file how should i create which has low similarity how should i create. 2.shall i can run modeller for the protein with high similarity by allowing modeller itself to create alignment thanks with regards arul

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Unknown residue type, position, sequence...
by 서주현 10 Mar '05

10 Mar '05

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Problem running modeller7v7
by sritin＠ibab.ac.in 09 Mar '05

09 Mar '05

Dear modeller users, I have just started using modeller version 7 on windows 98 platform having intel celeron processor. But the program doesnt run. It seems there is problem with installtion. Any command i type, it gives an error of "Bad command or file name". If i type any command from bin directory the error is as follow forrtl: severe (43): file name specification error, unit 11, file IMAGE PC ROUTINE LINE SOURCE MOD7V7.EXE 006BE729 Unknown Unknown Unknown MOD7V7.EXE 006BE587 Unknown Unknown Unknown MOD7V7.EXE 006BD764 Unknown Unknown Unknown MOD7V7.EXE 006BDB99 Unknown Unknown Unknown MOD7V7.EXE 006AF4D4 Unknown Unknown Unknown MOD7V7.EXE 004ED3A1 Unknown Unknown Unknown MOD7V7.EXE 004DE47B Unknown Unknown Unknown MOD7V7.EXE 006A542F Unknown Unknown Unknown MOD7V7.EXE 006EDB39 Unknown Unknown Unknown MOD7V7.EXE 006DC824 Unknown Unknown Unknown KERNEL32.DLL BFF8B560 Unknown Unknown Unknown KERNEL32.DLL BFF8B412 Unknown Unknown Unknown KERNEL32.DLL BFF89DD5 Unknown Unknown Unknown It will be great if someone can help me out as to where i have gone wrong. Thanks in advance. Ritin Sharma X-Ray Crystallography and Biophysics lab Department of Physics Indian Institute of Science

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Question about restraints
by akiheikk＠mappi.helsinki.fi 08 Mar '05

08 Mar '05

Hi, I'm a new modeller user trying to model some closely related proteins for docking purposes. I would like to model the binding site of the ligand as well as possible. The template file I'm using has the ligand in the binding site. I would like to know is there an easy way of setting the restraints for the most important residues? Should I use the MAKE_RESTRAINTS command somehow or is it more reliable to use another program like Sybyl or Insight to choose the restraints? Also the command SET HETATM_IO allways gives me an error: Number of residues in the alignment and pdb files are different: 280 282 Might this be related to the fact that there are two phosphorylated residues in the template? I would love to see a more thorough tutorial on modelling using restraints. [Aki] Aki Heikkilä Department of pharmaceutical chemistry University of Helsinki

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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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