Hi!Everybody:
Is there anybody who can correct this error for me?
My error messages are as following
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openf5__224_> Open 11 OLD SEQUENTIAL ./1DBG_A.pdb
rdpdb___303E> No atoms were read from the specified input PDB file:
1) Possibly because an incorrect/non-existent PDB file is specified.
2) Possibly because the segment is specified incorrectly in the
alignment file or by the TOP variable MODEL_SEGMENT. That is,
the beginning residue number and/or chain id in MODEL_SEGMENT
may not be found in the input PDB file; MODEL_SEGMENT: 1:
To find out more, switch on maximal output by 'SET OUTPUT_CONTROL = 1 1 1 1 2'
rdabrk__288W> Protein not accepted: 1
rdabrk__290E> Number of residues in the alignment and pdb files are different: 506 0
For alignment entry: 1
recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
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and my top file
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# Very fast homology modelling by the MODELLER TOP routine 'model'.
INCLUDE # Include the predefined TOP routines
SET ALNFILE = 'Together2.ali' # alignment filename
SET KNOWNS = '1DBG_A' '1AIR_' # codes of the templates
SET SEQUENCE = 'T0101' # code of the target
SET ATOM_FILES_DIRECTORY ='./:../atom_files' # directories for input atom files
SET STARTING_MODEL = 2
SET ENDING_MODEL = 2
SET OUTPUT_CONTROL = 1 1 1 1 2
# SET OUTPUT = 'LONG'
SET FINAL_MALIGN3D = 1
CALL ROUTINE = 'very_fast' # prepare for extremely fast optimization
CALL ROUTINE = 'model' # do homology modelling
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My alignment file
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>P1;1DBG_A
structureX:1DBG_A:1 : :506 : : : : :
----MKMLNKLAGYLLPIMVLLNVAPCLGQVVASNETLYQVVKEVKPGGLVQIADGTY--
-----KDVQLIVSNSGKSGLPITIKALNPGKVFFTGDAKVELRGEHLILEGIWFKDGNRA
IQAWKSHGPGLVAIYGSYNRITACVFDCFDEANSAYITTSLTEDGKVPQHCRIDHCSFTD
KITFDQVINLNNTARAIKDGSVGGPGMYHRVDHCFFSNPQKPGNAGGGIRIGYYRNDIGR
CLVDSNLFMRQDSEAEIITSKSQENVYYGNTYLNCQGTMNFRHGDHQVAINNFYIGNDQR
FGYGGMFVWGSRHVIACNYFELSETIKSRGNAALYLNPGAMASEHALAFDMLIANNAFIN
VNGYAIHFNPLDERRKEYCAANRLKFETPHQLMLKGNLFFKDKPYVYPFFKDDYFIAGKN
SWTGNVALGVEKGIPVNISANRSAYKPVKIKDIQPIEGIALDLNALISKGITGKPLSWDE
VRPYWLKEMPGTYALTARLSADRAAKFKAVIKRNKEH*
>P1;T0101
sequence:T0101:1 : :400 : : : : :
ADCSSDLTSGISTKRIYYVAPNGNSSNNGSSFNAPMSFSAAMAAVNPGELILLKPGTYTI
PYTQGKGNTITFNKSGKDGAPIYVAAANCGRAVFD----------FSFPDSQWVQAS---
--------------YGFYVTGDYWYFKGVEVTRAGYQGAYVIGSHNTFENTAFHHN----
----------RNTGLEINNG--GSYNTVINSDAYRNYDPKKNGSMADGFGP-KQKQGPGN
RFVGCRAWENSDDGFDLFDS--PQKVVIENSWAFRNGINYWNDSAFAGNGNGFKLGGNQA
VGN-------HRITRSVAFGNVSKGFDQNNNAGGVT---------------VINNTSYKN
GINYGFGSNVQSGQK----------------------HYFRNNVSLSASVTVSNADAKSN
SWDTGPAASASDFVSLDTSL------------------------ATVSRDNDGTLPETSL
FRLSANSKLINAGTKESNISYSGSAPDLGAFERN---*
>P1;1AIR_
structureX:1AIR_:1 : :353 : : : : :
---------ATDTGGYAATAGGNVTGAVSKTATSMQDIVNIIDAARLDANGKKVKG----
-----GAYPLVITYTGNEDSLINAAAAN--------------------ICGQWSKDPRG-
--------------VEIKEFTKGITIIGANGSSANFGIWIKKSSDVVVQNMRIGYLPGG-
----------AKDGDMIRVD--DSPNVWVDHNELFAANHECDGTPDN-----------DT
TFESAVDIKGASNTVTVSYN-----YIHGVKKVGLDGSSSSDTGRNITYHHNYYNDVNAR
LPLQ-------RGGLVHAYNNLYTNITGSGLNVRQN------------------GQALIE
NNWFEKAINPVTSRY--------------------------DGKNFGTWVLKGNNITKPA
DFSTYSITWTADTKPYVNAD---------------------------SWTSTGTFPTVAY
N----YSPVSAQCVKDKLPGYAGVGKNLATLTSTACK*
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My PDB files and sequences used in the alignment are all from PDB
Any help would be appreciated.
YeBin