- modeller_usage - salilab.org

Regarding manual protein sequence alignment
by rajesh rengaraj 15 Mar '05

15 Mar '05

Hi friends. I need help from our groups regarding the Protein manual sequence alignment.I modelled a protein which shows low Ramachandran plot validatity in order to increase this i have to do the manual alignment.I dont know what are the procedure for this and how to do this, whether it is depends upon the physico-chemical properties of amino acids or any other else. So Kindly do the needful. Take care. ________________________________________________________________________ Yahoo! India Matrimony: Find your life partner online Go to: http://yahoo.shaadi.com/india-matrimony

4 4

problem_again
by vivek sharma 14 Mar '05

14 Mar '05

Hello Benn, I am a regular user of MODELLER. I was using 6v2 before this but now I switched to 7v7. I got very strange errors, which I never got in 6v2. Could you please explain. I found some similar posts in concern to these, but no solutions. --------------log file output---------- assgn___547E> Incorrect element type for variable: OUTPUT_CONTROL Element, element type: 3 Command line: SET OUTPUT_CONTROL = 1 1 1 1 1 assgn___525E> Error in TOP variable assignment. assgn___547E> Incorrect element type for variable: LIBRARY_SCHEDULE Element, element type: 3 Command line: SET LIBRARY_SCHEDULE = 1 assgn___525E> Error in TOP variable assignment. assgn___547E> Incorrect element type for variable: DYNAMIC_COULOMB Element, element type: 3 Command line: SET DYNAMIC_COULOMB = ON assgn___525E> Error in TOP variable assignment. assgn___547E> Incorrect element type for variable: HETATM_IO Element, element type: 3 Command line: SET HETATM_IO = 'on' assgn___525E> Error in TOP variable assignment. assgn___544E> Variable name not recognized: ALNFILE Command line: SET ALNFILE = 'alignment.ali' assgn___525E> Error in TOP variable assignment. assgn___544E> Variable name not recognized: KNOWNS Command line: SET KNOWNS = 'hrc' assgn___525E> Error in TOP variable assignment. assgn___544E> Variable name not recognized: STARTING_MODEL Command line: SET STARTING_MODEL = 1 assgn___525E> Error in TOP variable assignment. assgn___544E> Variable name not recognized: ENDING_MODEL Command line: SET ENDING_MODEL = 5 assgn___525E> Error in TOP variable assignment. assgn___544E> Variable name not recognized: MD_LEVEL Command line: SET MD_LEVEL = 'refine_1' 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 Dynamically allocated memory at finish [B,kB,MB]: 56755 55.425 0.054 Starting time : 2005/03/14 11:07:32.511 Closing time : 2005/03/14 11:07:33.531 Total CPU time [seconds] : 0.99 ---------------------------------------- While model-default.top in examples runs perfectly alright. What can be the problem? Please suggest. br, Vivek -- VIVEK SHARMA HBG BI "You must be the change you wish to see in the world." MKG

3 2

Modeller7v7 on Fedora core 2
by Xiao-Ping Zhang 14 Mar '05

14 Mar '05

Dear Ben Webb and Modeller users, I installed modeller7v7 on my Fedora core 2 linux using modeller-7v7-1.rpm. When I tried to run a .top file which I used for modeller6v2, I got following error message. Could you give me some hints please? Thank you for your help. Sincerely, Xiao-Ping ########################## Kind, OS, HostName, Kernel, Processor: 4, Linux localhost.localdomain 2.6.5-1.358 i686 Date and time of compilation : 09/14/2004 11:06:39 Job starting time (YY/MM/DD HH:MM:SS): 2005/03/13 23:31:37.084 rdactio_534E> Command not recognized: recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 56755 55.425 0.054 Starting time : 2005/03/13 23:31:37.084 Closing time : 2005/03/13 23:31:38.334 Total CPU time [seconds] : 1.22 ############################ Xiao-Ping Zhang, PhD Section of Microbiology Division of Biological Sciences University of California, Davis Davis, CA95616 Phone: 530-7523016 (lab); 530-2975280 (home) Fax: 530-7529014 e-mail: xpzhang(a)ucdavis.edu

2 1

modeller running-help
by Elavazhagan 12 Mar '05

12 Mar '05

Hello wisdom, Glad to mail u. I am a stranger to this group. Let me know how to compille the modeller7v7 in REDHAT LINUX9.0,ie where should I put my input files either in examples or elsewhere and how can I refine the model using modeller. ur reply is mostly appreciated. Gratitude. -- E.Elavazhagan 09444332083

2 3

help
by arul prakasam 12 Mar '05

12 Mar '05

sir how to create pir format alignment file.i have done multiple sequence alignment with clustalx and had given the result msf format to genedoc and had export it to pir format what is this command "convertpir.pl [options] [pdbcode] [alignmentfile]" and how to get .ali file thanking u sir Yahoo! India Matrimony: Find your life partneronline.

1 0

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

2 1

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

1 0

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

10 Mar '05

2 1

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

2 1

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

2 1