[modeller_usage] help on using modeller

[rathan kar <>]

hi all

iam a fresher working on modeller and nothing is going on here properly . i use a win me machine with mod6v2 installed. i tried an alignment file to model but its not working .i have included the top files for reference

INCLUDE                             # Include the predefined TOP routines

SET OUTPUT_CONTROL = 1 1 1 1 1      # uncomment to produce a large log file
SET ALNFILE  = 'alignmentfile.ali'      # alignment filename
SET KNOWNS   = '1HM9'               # codes of the templates
SET SEQUENCE = 'query'               # code of the target
SET ATOM_FILES_DIRECTORY = 'c:/mod6v2/bin/1hm9.pdb'

 # 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)
CALL ROUTINE = 'model'              # do homology modelling

i dont know what does this atom_files mean.plz explain

the ERROR it shows is as follows:

openf5___224_>open         11       OLD         SEQUENTIAL     alignmentfile.ali

rdpir___376W>not enough fields in the sequence line of the sequence entry:sequence:query:1::165 : :

actual fields should be:          7               10

(Fields are separated by a colon. :)

read_al_375E>unknown residue type,Position , Sequence:          1       1

recover_____E>ERROR_STATUS=>STOP_ON_ERROR 1        1

 

Yahoo! India Matrimony: Find your partner online.