Hi!Everybody: Is there anybody who can correct this error for me? My error messages are as following __________________________________ 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 ___________________________________________________________ and my top file ___________________________________________________________ # 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 ________________________________________________________________ My alignment file ______________________________-- >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* ______________________________________________________ My PDB files and sequences used in the alignment are all from PDB
Any help would be appreciated.
YeBin