February 2004 - modeller_usage

FAD / FeS topology ?
by Guenter Fritz 19 Feb '04

19 Feb '04

Dear all, I want to include an FAD and a FeS cluster into the modelling. However these residues / heteroatoms have no entry in the topology of modeller. Did anyone create topology files / patches for a flavin or FeS cluster ? Best regards guenter -- *********************************** Dr. Guenter Fritz Fachbereich Biologie Sektion Naturwissenschaften Universitaet Konstanz Universitaetsstrasse 10 Postfach M665 D-78457 Konstanz e-mail: Guenter.Fritz(a)uni-konstanz.de Tel.: +49-(0)7531 88 3687 Fax: +49-(0)7531 88 2966

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Second_line_of_the_alignment
by "Chupakhin - Чупахин" 19 Feb '04

19 Feb '04

Dear my Modeller! Would you help with that problem: How must look second line of the alignment when I'm using pentamer for modeling pentamer? does have any special?

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begginer
by "Chupakhin - Чупахин" 17 Feb '04

17 Feb '04

Dear modeller... ..here is mine TOP file, I've tried to align it with both pdb from Brookheaven and genereted by Sybyl (free of hetero atoms and Ca) but it fails... ERROR: dispers_247E> internal error : 1263 1267 recover____E> ERROR_STATUS >= STOP_ON_ERROR INCLUDE SET RR_FILE = '$(LIB)blosum62.sim.mat' SET ATOM_FILES_DIRECTORY = './' READ_MODEL FILE = '1I9B.pdb' SEQUENCE_TO_ALI ALIGN_CODES = '1I9B', ATOM_FILES = '1I9B.pdb' READ_ALIGNMENT FILE = 'xxxx.ali', ALIGN_CODES = ALIGN_CODES 'XXXX', ADD_SEQUENCE = ON ALIGN2D WRITE_ALIGNMENT FILE='xxxx_aln.ali', ALIGNMENT_FORMAT = 'PIR' PDB file have 5 subunits and I try to align it...failed Could I use another alignment programm? and hand-make my own alignment file? (I've tried one but it fails...) Could you look at the alignment and top file??? INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # comment to produce a large log file SET ALNFILE = 'xxxx_ach.ali' # alignment filename SET KNOWNS = '1I9B.pdb' # codes of the templates SET SEQUENCE = 'XXXX' # code of the target SET ATOM_FILES_DIRECTORY = './' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model CALL ROUTINE = 'model' # do homology modelling STOP >P;1I9B structureX:1I9B: 1 :A: 1025:E:undefined:undefined:-1.00:-1.00 >P;XXXX sequence:XXXX: : : : ::: 0.00: 0.00

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docking
by Jaimin Shah 17 Feb '04

17 Feb '04

Hello MODELLER users, I have been able to generate models for my protein, thanks to the guidance received here. Can someone please tell me how I should dock the substrate to my enzyme? Sincerely, Jaimin Shah M.Sc. (Biotechnology) School of Biosciences & Bioengineering I.I.T. Bombay

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error in restraints calculation
by David Giganti 17 Feb '04

17 Feb '04

GOOD MORNING, MY MODELLER'S RUN WAS STOPPPED WHEN IT WAS CALCULATING THE RESTRAINS !!! SOMEBODY COULD EXPLAIN TO ME THE CAUSES OF THIS FAILURE. THANK YOU. r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 crsplin_459E> Increase MAXSPL to at least 1074 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 218439351 213319.700 208.320 Starting time : 2004/02/17 16:16:21.633 Closing time : 2004/02/17 16:18:53.259 Total CPU time [seconds] : 53.72

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Fortran Runtime Error
by Zoee Gokhale 15 Feb '04

15 Feb '04

Hi, Running MODELLER 6v2 on my Linux PCC (Red Hat 7.2) gives me the following error ? FORTRAN Runtime Error: ? Attempt to read past end of file ? READ(UNIT=11,... Please help me solve this problem. Thanks, Zoee Gokhale ___________________________________________________________ BT Yahoo! Broadband - Free modem offer, sign up online today and save £80 http://btyahoo.yahoo.co.uk

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[Mailman] request letter for vlarification of a doubt regarding modelling
by anthony johnson 12 Feb '04

12 Feb '04

dear sir, Iam a student of Bioinformatics and iam trying to do my protein modelling work on a tat protein of Hiv and from the 3DPSSM and my blast results i have found one template with good percentage of homology with my query. i retrieved the PDB of it to use it as the Atom file for submitting it to the modellor software that we have in our academic institute.But the problem was that the PDB was to be found as the NMR structure which was predicted to have 8 different models and the ID of the PDB is 1tvs and now iam in the confusion state that which model i have to choose as my atom file for submission to modellor software.Not only this hit, but most of my template hits are NMR structures and they too show me the same type of models.i came to view the site of modellor and i have found your mail ID , so iam mailing you my problem. And i humbly request you to show me a solution to this problem as i couldnt find any one who to help over here.hoping your kind favour in this regard. Awaiting your early reply. thanking you sir, Anthony Johnson anthony_johnson(a)rediffmail.com _______________________________________________ Mailman mailing list Mailman(a)salilab.org http://salilab.org/mailman/listinfo/mailman

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[modeller_usage] Request for a doubt clarification regarding modelling
by anthony johnson 12 Feb '04

12 Feb '04

Iam a student of Bioinformatics and iam trying to do my protein modelling work on a tat protein of Hiv and from the 3DPSSM and my blast results i have found one template with good percentage of homology with my query. i retrieved the PDB of it to use it as the Atom file for submitting it to the modellor software that we have in our academic institute.But the problem was that the PDB was to be found as the NMR structure which was predicted to have 8 different models and the ID of the PDB is 1tvs and now iam in the confusion state that which model i have to choose as my atom file for submission to modellor software.Not only this hit, but most of my template hits are NMR structures and they too show me the same type of models.i came to view the site of modellor and i have found your mail ID , so iam mailing you my problem. And i humbly request you to show me a solution to this problem as i couldnt find any one who to help over here.hoping your kind favour in this regard. Awaiting your early reply. thanking you sir, Anthony Johnson Yahoo! India Education Special: Study in the UK now.

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Re: [modeller_usage] divide__213E> Division by zero, during seq. search
by Esben Jannik Bjerrum 11 Feb '04

11 Feb '04

Well, your superstition isn't wrong, All characters needs to be UPPERCASE. Strange though that its halfway through the database that it fails when they are lowercase. Thanks for the help Esben

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COMMAND line clarification
by Nataraj Balkrishnan 10 Feb '04

10 Feb '04

Dear modeller, what is the significance of the line SET STARTING_MODEL= 1 SET ENDING_MODEL = 1 in modeling top file ,what that command and associated number indicates. yours, B.Nataraj --------------------------------- Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now

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