Hi there,
I have had this problem before myself and the advice given is as follows.
Ensure that your naming of your template and model is consistent thruout
the top and ali file. eg you should have:
>P1;1ajs
structureX:1ajs:1:A; etc ...(not p1ajs)
you alkso have a lot of ":" in your seuqnece line (probably too many)
Try this and see how you go
J
서주현 wrote:
> Dear Modellers,
>
> I've faced an error with same error message that I met before.
>
> I can't figure out the error in my input files.
>
> .ali file is generated by THREADER (by D.T. Jones).
>
> .ali, .top and log file are described below.
>
> Any help or comment will be much appreciated.
>
> Thank you.
>
>
> Ali file
>
>>P1;1ajs
> structureX:p1ajs:1:A:412:A:PDB::0.00:0.00
> --APPSVFA-E-VPQAQPVLVFKLIADFREDPDPRKVNLGVGAYRT-DDCQPWVLPVVRKVEQRIANNSSL-------NHEYLPILGLAEFRTCASRLALG-DDSPALQEKRVGGVQSLGGTGALRIGAEFLARWYNGTNNKDTPVYVSSPTWENHNGVFTTAGFKDIRSYRYWDTEKRGLDLQGFLSDLENA-PEFSIFVLHACAHNPTGTDPTPEQWKQIASVMKRRFLFPFFDSAYQGF--ASGNLEKDAWAIRYFVSEGFELFCAQSFSKNFGLYNERVGNLTVVAKEPDSILRVLSQMQKIVRVTWSNPPAQGARIVARTLSDPELFHEWTGNVKTMADRILSMRSELRARLEALK----TPGTWNHITDQIGMFSFTGLNPKQVEYLINQKHIYLLPSGRINMCGLTTKNLDYVATSIHEAVTKIQ*
>>P1;SEQ
> sequence::::::SEQ::0.00:0.00
> MFKSMIMAPPDPILGLSKI--------YHSDTKKNKINLGIGVYIEKFHAAPILE-SVKQAEDLLLKKEISKNYLAIEGSNDFNNANQ--------TLLFGPNDS-IISKNRIRTVQAPGGTGALRIAAECIAKYDNTINKKRRI-WISEPSWVNHKNIFFAAGLEVCTYPYYQKSTHS-IEFDKLIDTFNNIVKPGDIVLLHGCCHNPTGMDPTIEQWKMLSECAEKNRWIPLFDLAYQGFDNGLQE---DLIGLHMFCKNNPELIVCNSYSKNFGLYNERVGACTIITENNNHADCVLSQLRATIRAIYSNPPAHGAAIVSTILQNKTLRFIWEKELKNMRDHIKNMRKLLFNTLNKYKNSKVINQDFSFINNQKGMFAYIGLNSNQVIKLREELGIYLVDSGRLNLAGLSHKNIDYICNAICNLYI---*
>
>
>
>
> Top file
>
> INCLUDE
> SET OUTPUT_CONTROL = 1 1 1 1 1
> SET ALNFILE = 'model.ali'
> SET KNOWNS = '../pdb/pdb1ajs.ent'
> SET SEQUENCE = 'SEQ'
> SET STARTING_MODEL = 1
> SET ENDING_MODEL = 1
> SET HETATM_IO = off
> SET WATER_IO = off
> SET LOOP_MD_LEVEL = 'refine_1'
> SET MD_LEVEL = 'refine_1'
> CALL ROUTINE = 'model'
>
>
>
> log file
>
> Dynamically allocated memory at amaxseq [B,kB,MB]: 2205269 2153.583 2.103
> openf5__224_> Open 11 OLD SEQUENTIAL model.ali
>
> Dynamically allocated memory at amaxbnd [B,kB,MB]: 8512161 8312.657 8.118
> openf5__224_> Open 11 OLD SEQUENTIAL model.ali
> read_al_375E> Unknown residue type,position,sequence: 1 1
> recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
>
> Dynamically allocated memory at finish [B,kB,MB]: 8512161 8312.657 8.118
> Starting time : 2005/03/10 22:34:12.278
> Closing time : 2005/03/10 22:34:13.182
> Total CPU time [seconds] : 0.87
>
>
>
> Joo-Hyun Seo,
>
> Molecular Biotechnology & Biomaterials Lab.,
>
> School of Chemical Engineering,
>
> Seoul National University
>
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--
Joel Tyndall, PhD
Lecturer
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University of Otago
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