- modeller_usage - salilab.org

mutation
by Jaimin Shah 23 Feb '04

23 Feb '04

Hello Dr. Owen. I am sorry I did not explain well. I am not able to compute H-bonds using Swiss-PDBViewer and I am getting "Unrealistic B-factor 0.0" in the log file of the mutant protein. (I had generated the mutant protein using the MUTATE_MODEL command of MODELLER.) Any suggestions will be appreciated. > Hi Jaimin, > > What do you mean by compute H-bonds? If you mean you want to add hydrogen > atoms and calculate some kind of energy i'd suggest using a molecular > mechanics program such as CHARMM. Hope this is of help! > > Owen > > > Sincerely, Jaimin Shah M.Sc. (Biotechnology) School of Biosciences & Bioengineering I.I.T. Bombay

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How to correct Bumps
by Nataraj Balkrishnan 21 Feb '04

21 Feb '04

Dear modellers, My modelled protein having error of bumps(non bonded atomic condact) for some about 10 atom positions according to What IF error report. What is the appropriate TOP script or routine to correct those error(bumps) causing atom postions ? Thank you in advance, Yours B.Nataraj --------------------------------- Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now

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modeling homotetramers
by Han Choe 20 Feb '04

20 Feb '04

Dear Modellers, I'm new to the modeller and recently made a single peptide model using the program successfully. Now I'm interested in building a model of a potassium ion channel whose structure is known to be a homotetramer. What is an easy way to build a model of those multmer proteins? Cheers, Han

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unrealistic B-factor 0.00
by Jaimin Shah 20 Feb '04

20 Feb '04

Please also tell me why I am getting "Unrealistic B-factor 0.00" in the log file of my mutant model. Thanking you, Sincerely, Jaimin Shah M.Sc. (Biotechnology) School of Biosciences & Bioengineering I.I.T. Bombay

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mutation
by Jaimin Shah 20 Feb '04

20 Feb '04

Dear all, Please provide ur suggestions. I mutated my models using the MUTATE_MODEL command. But the model I get, I can not compute H-bonds in it at all. Any possible explanations? Sincerely, Jaimin Shah M.Sc. (Biotechnology) School of Biosciences & Bioengineering I.I.T. Bombay

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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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