Dear sir,

I am facing a problem in getting my model of an allosteric enzyme and the prblem is with the count in the pdbfile and the alignment file

the top file i am using is as follows: # Homology modelling by the MODELLER TOP routine 'model'.

INCLUDE # Include the predefined TOP routines

SET OUTPUT_CONTROL = 1 1 1 1 2 # uncomment to produce a large log file SET ALNFILE = 'template.ali' # alignment filename SET KNOWNS = '1BDG' '1DGK' '1CZA' 1BG3' '1HKC' ' # codes of the templates SET SEQUENCE = '1Str' # code of the target SET ATOM_FILES_DIRECTORY = '/disk1/project/ratnesh/pdbfiles' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate) SET HETATM_IO = on # include heteroatom in the model #SET WATER_IO = on CALL ROUTINE = 'model' # do homology modelling

and the error i am getting in logfile is as follows:

Read the alignment from file : templatefile.ali Total number of alignment positions: 953

# Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1HKB 905 3 1HKB undefined 2 1DGK 903 3 1DGK undefined 3 1CZA 903 3 1CZA undefined 4 1BG3 893 3 1BG3 undefined 5 1HKC 901 3 1HKC undefined 6 1Str 493 1 1Str Candida albicans TOP_________> 122 107 CHECK_ALIGNMENT

check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL /disk1/project/ratnesh/pdbfiles/1HKB.pdb openf5__224_> Open 11 OLD SEQUENTIAL /disk1/project/ratnesh/pdbfiles/1DGK.pdb rdabrk__291E> Sequence difference between alignment and pdb :

STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*----- 2 902 33 GLYP 113 ADP RTppp## rdabrk__288W> Protein not accepted: 2 openf5__224_> Open 11 OLD SEQUENTIAL /disk1/project/ratnesh/pdbfiles/1CZA.pdb rdabrk__291E> Sequence difference between alignment and pdb :

STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*----- 3 903 33 GLYP 113 ADP Tpppp# rdabrk__288W> Protein not accepted: 3 openf5__224_> Open 11 OLD SEQUENTIAL /disk1/project/ratnesh/pdbfiles/1BG3.pdb openf5__224_> Open 11 OLD SEQUENTIAL /disk1/project/ratnesh/pdbfiles/1HKC.pdb fndatmi_285W> Number of residues <> number of atoms; atom code: 905 901 CA check_a_337E> Structure not read in: 2 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1

Dynamically allocated memory at finish [B,kB,MB]: 20689357 20204.449 19.731 Starting time : 2004/03/29 17:26:50.612 Closing time : 2004/03/29 17:27:04.831 Total CPU time [seconds] : 0.00

Can u help in sorting out what is this error and how it can be solved

warm regards hemant

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