Re: [modeller_usage] help on using modeller

[Nataraj Balkrishnan <>]

Hi Rathan ,

       The problem lies in  your alignment file. Try to verify it with the one given in modeller example. if still cant fix problem. mail your alignment file......without seeing alignment file it's difficult to fix problem,

 

Yours ,

B.Nataraj

rathan kar <> wrote:

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

 

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B.Nataraj,
Final year M.Tech.(Bioinformatics),
SASTRA Deemed University,
(www.sastra.edu)
Thanjavur,
Tamil Nadu,
India.
Email:
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