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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