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
# 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