modeller_usage March 2005

modeller_usage@salilab.org

30 participants
29 discussions

Re: modeller_usage Digest, Vol 4, Issue 21
by drugdesign 17 Mar '05

17 Mar '05

You can use Autodock program. It's a free software for docking studies. All the best! Andrew >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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USING OF RESTRAIN FILE 'RSR' FOR OPTIMISATION OF MODEL
by apurba kumar samal 17 Mar '05

17 Mar '05

Respected Sir, Myself Apurba Kumar Samal, student of indian institute of information technology Allahabad. Sir I am doing my project on structure of Falcipain-3, a cystiene protease from PLASMODIUM FALCIPARUM.I am using your software for modelling,MODELLER7v7. When i verify the structure by verification server it shows deviation in bone length. For rectification i tried to use bond restrain. It gives the x.rsr files. I could not understand how can I use that file to rectify my model. How can I use that file to rectify my model. what are the command i have to use this file on my predicted structure.Sir my work has now stopped for that please sir help me how to move further. Waiting for your positive and early response. Thanking you. Apurba Kumar Samal. M.Tech. Bioinformatics, IIIT-A asamal_bi03(a)iiita.ac.in

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how can i apply 'rsr' file for optimisation of my model
by apurba kumar samal 17 Mar '05

17 Mar '05

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version 6 and 7 scripts
by Paula R.=?ISO-8859-1?Q?_Kuser_Falc=E3o?= 16 Mar '05

16 Mar '05

Dear Modeller I was using the script Align2D.top below to run modeller with version 6.2. Now that we installed version 7, I just can't get it to work. I get the following message: read_al_375E> Unknown residue type,position,sequence: 1 2 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Could you please let me know what is wrong? Thanks, Paula Kuser Align2D.top ############################################# # ALIGNING OUR TARGET WITH THE TEMPLATE # # file.pdb - your template pdb file # pdb name - template code # seq.txt - target file in pir format # seq - target code # file.ali - constructed alignment file ############################################# # Include MODELLER library scripts #INCLUDE # Defining our local pdb directory for input #SET ATOM_FILES_DIRECTORY = '/db/pdb' # Reading template pdb file READ_MODEL FILE = '1ig8.pdb' # Defining code of the template SEQUENCE_TO_ALI ALIGN_CODES = '1ig8' # Reading our target READ_ALIGNMENT FILE = 'seq.txt', ALIGN_CODES = ALIGN_CODES 'HEX', ADD_SEQUENCE = on # Alignment ALIGN2D # Alignment in pir formate WRITE_ALIGNMENT FILE='HEXTC.ali', ALIGNMENT_FORMAT = 'PIR' Here is the seq.txt file: ######################################################### # #TARGET SEQUECE IN PIR FORMAT # ########################################### >P1;HEX sequence:HEX:.:.:.:. MSARLNNLLQHIAVKDKDSDTMRHLKQRMALASLANQFTVGKDHLKQLMLYMVHQMIEG LEGRESTLRMLPSYVYKTDPSKATGVFYALDLGGTNFRVLRVTCKEGRVADRVDAKFVI PQQALQGTAEDLFGFIAQSVKKMMEQKAPEDLNRTVPLGFTFSFPTEQKGVDHGFLIKW TKGFSTRGVEGKDVVELLQKALKRMEVKVKVVALCNDTVGTLITNYFFDPDTQVGVIIG TGSNACYFEDAYAVTKEPSVAARGTTQTPINMECGNFDSKYKFVLPVTAYDEAMDAVTP NRNFQTQEKMVSGMYLGEISRRMIAHLAELHCLPSALASKMAKPWSFETKFMGMISADR MPGLQFTRQVFQELFQVDVTDVADLHVIRDVCCLVRGRAAQISAMFCSAPLVKTRKEGR ATVAIDGSVFEKTPSFRRLLQQNMNAILGPGCDVTTALARDGSGIGAAFISALVVNDK* Paula Kuser Falcão Laboratório de Bioinformática Estrutural Embrapa Informática Agropecuária -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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Thanks to our groups for quick response
by rajesh rengaraj 16 Mar '05

16 Mar '05

Dear friends, Thanks for sharing your valuable time with me and your quick response for my queries. You brought me out from the darkness. Thank you. Yahoo! India Matrimony: Find your life partneronline.

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Regarding manual protein sequence alignment
by rajesh rengaraj 16 Mar '05

16 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

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problem_again
by vivek sharma 15 Mar '05

15 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

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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

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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

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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.

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modeller_usage March 2005