modeller_usage March 2004

modeller_usage@salilab.org

25 participants
30 discussions

modeller errors
by kambhampati anjaneyulu 28 Mar '04

28 Mar '04

Respected sir ; how to run the programme in windows xp sysytem . which commnand i have to use .and how to run the programme.please clarify my doubts --------------------------------- Do you Yahoo!? Yahoo! Finance Tax Center - File online. File on time.

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Re: [modeller_usage] side-chain torsion angles
by Eric Feyfant 26 Mar '04

26 Mar '04

Hi Liu; I just want to add a comment to what Mickael just told you. Basically, Modeller use spatial restraint derived from the homology, which means that it will derive the restraint for the side chain from the residues in the template with which is aligned. Modeller has a table for equivalent position between residues: example Alanine and Lysine will share as equivalent backbone atoms and the Calpha . This means that if your template is Ala and your target is Lysine, only homology restraint concerning backbone + Calpha will be derived from the Ala and applied to the Lysine. That implies that your Lysine side chain will be optimize with non homology derived restraints (i.e. those from template),and so more dependent on the starting conformation, the environment and, the potential your are using. At the opposite if you check the identical residues you should see less fluctuation. Best Eric. >>> Mickael Krzeminski <mkrzemin(a)pasteur.fr> 3/26/2004 6:23:57 AM >>> Liu, Your problem deals essentially with side chains. You have to know that all programs of homology modeling have difficulties for prediction of side chains and results are often bad... Basically, at the biginning, programs choose conformation of side chains of templates in conditon that the same residuse are aligned. If it is not the case, the side chain is placed and is minimized. So, it is logical whether your side chains are different between your models because the minimization depends on the local environnement. I hope you have understood what i had tried to explain... With regards, Mickaël On Wed, 24 Mar 2004, Binbin Liu wrote: > Hi there, > I got one hunderd models. The side-chain torsion angles of the interesting > residues are vary. Does anybody know why. Does MODELLER calculate the torsion > based on some rules or it is by chance. > > > Cheers > > > BinBin > _______________________________________________ > modeller_usage mailing list > modeller_usage(a)salilab.org > http://salilab.org/mailman/listinfo/modeller_usage > _______________________________________________ modeller_usage mailing list modeller_usage(a)salilab.org http://salilab.org/mailman/listinfo/modeller_usage

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side-chain torsion angles
by Binbin Liu 26 Mar '04

26 Mar '04

Hi there, I got one hunderd models. The side-chain torsion angles of the interesting residues are vary. Does anybody know why. Does MODELLER calculate the torsion based on some rules or it is by chance. Cheers BinBin

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OBJECTIVE FUNCTION
by Matthias 26 Mar '04

26 Mar '04

-- NeoMail - Webmail that doesn't suck... as much. I took several runs on Modeller and gaint 2 models.Further I otpimized these models by loop modelling and this final loop models present a very low, regarding to the other, OBJECTIVCE FUNCTION. But, my question: is this objective function relates only to the loop models or is it a value for the global model? Further: does anybody know if there should be great differences in performin a modeller job in one or two top scripts.. it seems to work better when splitted, why? Thxs a lot , Matthias Negri Diploma student

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Number problem
by hemant kushwaha 24 Mar '04

24 Mar '04

Dear sir, I am trying to model a allosteric protein, my problem is that the number of residues in alignment file(with template and target sequence) and pdb file is different b'cos in PDB file there is a gap in the atoms and HETATM. So modeller is giving error at check alignment, and giving no. of residues in alignment and pdb file are different. Can you please give me any suggestion or advice how to sort this problem with regards Hemant __________________________________ Do you Yahoo!? Yahoo! Finance Tax Center - File online. File on time. http://taxes.yahoo.com/filing.html

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FORTRAN runtime errors...and more
by Matthias 22 Mar '04

22 Mar '04

-- Hello, I'm Matthias! I have more then one question, so far: - How do I use the "user_after_singel_model" subroutine, for ex. to compare the model with an X-ray structure? Can you send me a sort of top.script, or at least, can you someone give me a hint? - Further, can you please check my top.script , please? I can't undestand why it sometimes doesn't work (.. it clashed more than once... and it appeared the message: FORTRAN runtime error: INQUIRE(UNIT=/usr/bin/mod6v2: line 38: 25355 segmentation fault (core dumped) $nice ${executable} $STEERF >$LOGF Can you explain me, what this mean? - I have some problems, in loop modelling, regard DEFINE_SYMMETRY.. my loops almost often aren't symmetric.. how can i solve it .. is it enough to call the 'def_sym' routine and fix SEG1 & SEG2? - At last but not least, how can i eliminate the error: "Array too small. Increase MPAIRS" or "Array too small. Increase MAXATM", and what's the reason for it? I know i'm askingyou a lot, but i hope someone can help me..... faithsfully Matthias Negri Diploma Student in Medicinal Chemistry at University of Bologna thias(a)scafrm.unibo.it P.S. i send you my tops: job.top --> JOB_28_125.pir, prova2.top, try.top --> Thias1.pir,

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Atom index is out of bounds error
by Han Choe 22 Mar '04

22 Mar '04

Dear All, I get the following error message and I don't understand how it arises. csrrng__299E> Atom index is out of bounds: 3015 3014 Cheers, Han

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problems with the MALIGN command
by Stefanie Offermann 19 Mar '04

19 Mar '04

hello, I would like to do another modeling procedure with two of my recent models as templates, so all the three sequences (2 structures, 1 sequence) in the aln-file are identical. to make a structural alignment of the 2 models I have used the command MALIGN with the following .top-script: ---------------------------------- # Read the sequences of structures from the specs in SEGFILE: READ_ALIGNMENT FILE = 'x.ali', ALIGN_CODES = 'all' # do a multiple sequence alignment of structures: MALIGN GAP_PENALTIES_1D = -600 -400 # do a multiple structural alignment of structures: MALIGN3D GAP_PENALTIES_3D = 0.0 3.0, WRITE_FIT = ON, WRITE_WHOLE_PDB = OFF, FIT_ATOMS = 'CA' # align the last sequence with the fixed alignment of structures: ALIGN GAP_PENALTIES_1D = -600 -400 # write the alignment to a file ALNFILE WRITE_ALIGNMENT FILE = 'out.aln', ALIGNMENT_FORMAT = 'ALN' ------------------------------------------------------------ after a few seconds the run stops with the following message in the log-file: --------------------------------------------------------------------------- Multiple dynamic programming alignment (MALIGN): Residue-residue metric : ${MODINSTALL6v2}/modlib//as1.sim.mat ALIGN_BLOCK : 1 Gap introduction penalty: -600.0000 Gap extension penalty : -400.0000 Length of alignment : 358 fndatmi_284E> Beginning atom index for a residue out of bounds: 0 0 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 ----------------------------------------------------------------- is there anybody who could explain me what I have to change ?? thank you! Steffi

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symmetrisation of models
by Binbin Liu 19 Mar '04

19 Mar '04

Hello there, My model is composed by several identical chains, but I find they are not really identical in 3D. How can I symmetrise them? Does anybody know any informatics? Many thanks. BinBin

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Search sequence in modeller not responding...!
by Nataraj Balkrishnan 18 Mar '04

18 Mar '04

Dear Modellers, I tried to search my sequence aganist the Modeller chain database. But my top file containing the search commands did not yield me any result after long time run. Here I pasted my topfile,alignment Top File SET SEARCH_RANDOMIZATIONS = 10 SET FILE = 'gam.ali' SEQUENCE_SEARCH ALIGN_CODES = 'gam' alignment file: >P1;gam sequence:gam:1 : :136 : : LNLLISIMGRTMGALGNLTFVLCIIIFIFAVMGMQLFGKNYVDNVD RFPDHDLPRWNFTDFMHSFMIVFRVLCGEWIESMWDCMLVGDVSCI PFFLATVVIGNLVVLNLFLALLLSNFGSSSLSAPTADNDTNKIA* The logfile did not contain any messages other than usual Heading that appear in all logfiles. Kindly help me. Yours, B.Nataraj --------------------------------- Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now

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modeller_usage March 2004