hi all am having a problem in modelling a protein, plz help
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HI ALL Iam modelling a protein in which iam encountering the errors as shown in the below log file. i have tried all hte possible things, but couldnt get the output. i have checked even the pdb files for the residues numbering and if any missing residues are present. but still couldnt model it. plz help.
TOP_________> 116 756 CALL ROUTINE = 'model'
TOP_________> 117 419 CALL ROUTINE = 'getnames'
TOP_________> 118 534 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL'
TOP_________> 119 535 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; '
TOP_________> 120 536 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE
TOP_________> 121 537 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE
TOP_________> 122 538 SET ROOT_NAME = SEQUENCE
TOP_________> 123 539 RETURN
TOP_________> 124 420 CALL ROUTINE = 'homcsr'
TOP_________> 125 112 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE
Dynamically allocated memory at amaxseq [B,kB,MB]: 145831 142.413 0.139 openf5__224_> Open 20 OLD SEQUENTIAL alignm.ali
Dynamically allocated memory at amaxbnd [B,kB,MB]: 8701803 8497.854 8.299 openf5__224_> Open 20 OLD SEQUENTIAL alignm.ali
Read the alignment from file : alignm.ali Total number of alignment positions: 357
# Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 2PIA 157 1 2PIA Oxido 2 1GVH 50 1 1GVH oxido 3 1TVC 64 1 1TVC oxidored 4 1TXC 34 1 1TXC oxidored 5 1KRH 43 1 1KRH Oxidored 6 1QGA 38 1 1QGA oxidored 7 1H42 45 1 1H42 ZNFING 8 1FNC 48 1 1FNC ZNFING 9 2PDA 92 1 2PDA Oxido 10 1RFK 88 1 1RFK ZNFING 11 reduct 350 1 reduct TOP_________> 126 113 STRING_IF STRING_ARGUMENTS = TOP_VERSION 'accelrys', OPER; ATION = 'ne', THEN = 'GO_TO __ACCELRYS1'
TOP_________> 127 117 CHECK_ALIGNMENT
check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL ./\2PIA.pdb openf5__224_> Open 11 OLD SEQUENTIAL ./\1GVH.pdb openf5__224_> Open 11 OLD SEQUENTIAL ./\1TVC.pdb openf5__224_> Open 11 OLD SEQUENTIAL ./\1TXC.pdb openf5__224_> Open 11 OLD SEQUENTIAL ./\1KRH.pdb rdabrk__290E> Number of residues in the alignment and pdb files are different: 43 33 For alignment entry: 5 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Dynamically allocated memory at finish [B,kB,MB]: 8703453 8499.466 8.300 Starting time : 2005/09/22 15:44:22.046 Closing time : 2005/09/22 15:44:23.250 Total CPU time [seconds] : 1.20
>P1;2PIA StructureX:2PIA :8: :164: :Oxido:HUM: : FLRLKIASKEKIARD--IWSFELTDPQGAPLPPFEAGANLTVAVPNGS---RRTYSLCNDS QERNRYVIAVKRDSNGRGGSISFIDDTSEGDAVEVSLPRNEF---PLDKRAKSFILVAGGI GITPMLSMARQ-LR--AEGLRSFRLYYLTRDPEGTAFFDELTS--DEW------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------* >P1;1GVH StructureX:1GVH :212: A :261:A :oxido:uk2: : ------------------------------------------------------------P D-GKGYRIAVKREEGGQVSNWLH-NHANVGDVVKLVAPAGDFFMAVADDTP---------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------* >P1;1TVC StructureX:1TVC :45:A:108:A :oxidored:uk3: : ---------------------------------FEPGQFMDLT--IPGTDVSRSYSPANLP NPEGRLEFLIRVLPEGRFSDYLRNDARVGQVLSVKGPL----------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------* >P1;1TXC StructureX:1TXC :216:A:249:A :oxidored:uk3: : ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------LCGPPGMID-AACELVRSRGIPGEQVF FEKF---LPSG-------------------------------------------------- ------------------------------------------------------* >P1;1KRH StructureX:1KRH :295:B: 327:B :Oxidored:uk4: : ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ----------------------WLNGGEVDV--YLCGPVPMVE-AVRSWLDTQGIQPANFL FEKFSAN------------------------------------------------------ ------------------------------------------------------* >P1;1QGA StructureX:1QGA :194:A :231:A :oxidored:uk6: : ------------------------------------------------------------- ------------------------------------------------------------- ------------------------LFLGVPTSSSLLYKEEFEKMKEKAPENFRLDFAVSRE Q------------------------------------------------------------ ------------------------------------------------------------- ------------------------------------------------------* >P1;1H42 StructureX:1H42 :190:A :235:A :ZNFING:HUM: : ------------------------------------------------------------- ------------------------------------------------------------- ------------------------LVFGVPTTPNILYKEELEEIQQKYPDNFRLTYAISRE QKNPQ--GGR--------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------* >P1;1FNC StructureX:1FNC :234: :281: :ZNFING:HUM: : ------------------------------------------------------------- ------------------------------------------------------------- ----------------------------------------------------------SRE QTNEKGEKMYIQTRMAQYAVELWEMLKKDNTYVYMCGLKG-MEKGI--------------- ------------------------------------------------------------- ------------------------------------------------------* >P1;2PDA StructureX:2PDA :229: :320: :Oxido:HUM: : ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------NTNARENTPFTVRLSRSGTSFEIPANRS--ILEVLRDANVRVP SSCESGTCGSCKTALCSGEADH-RDMVLRDDE--KGTQIMVCVSRAKSAELVLD* >P1;1RFK StructureX:1RFK :204: B :291:B :ZNFING:HUM: : ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- ------------------------------------------------------------- --------------------------KVTLINEAEGLNKTIEVPDDQYILDAAEEAGIDLP YSCRAGACSTCAGKLISGTVDQSDQSFLDDDQIEAGYVLT-CVAYPTSDCVIET* >P1;reduct Sequence:reduct:1::350::::: FHDMRVASVRPETRDAIVVTFDVP-PSLADSFHYAPGQHLTLRTEIGGEDVRRSYSICSGA D-ERALRIAIKRVHGGLFSNWAN-DFMKPGVSVEVMPPSGHFGVAPDPQHHRNYAAFAAGS GITPILSQIKTILA--AEQGSRFTLVYGNRSSSSVMFREELADLKDQYGERLNLVHVLSRE QQDIELFNGRIDRERCDALLTRWIDAKRID-VAFICGPMDMME-AVSASLQAHGVAKSAIK MELFATSLPKGPRPVHSHPVKGTEDCEVTVIQDGRVRQFTMPKNRDS-VLDAGLGQGIEMP YSCKGGVCSTCRCKVIDGEVDHDTNFALEDYEIARGFRLS-CQSYPVTDKLVLD*
# A sample TOP file for fully automated comparative modeling
INCLUDE # include MODELLER routines
SET ATOM_FILES_DIRECTORY = './:../HYPO' # directory with input atom files
SET ALNFILE = 'alignm.ali' # input file w/ templates and target
SET KNOWNS = '2PIA' '1GVH' '1TVC' '1TXC' '1KRH' '1QGA' '1H42' '1FNC' '2PDA' '1RFK' # templates' PDB codes
SET SEQUENCE = 'reduct' # target code
SET STARTING_MODEL = 1
SET ENDING_MODEL = 3
SET HETATM_IO = ON
SET OUTPUT_CONTROL = 1 1 1 1 1
CALL ROUTINE = 'model' # get alignment and a model