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Re: Running MODELLER



Hi,

It looks like you :
1. didn't installed MODELLER correctly
2. didn't source .cshrc after installation

Please, email me a copy of your .cshrc and all input files.

Thanks,
Bozidar

PS. I implore everybody to email all the questions to the modeller_usage
list first, because some other people might have the same problems and
they could help or learn how to solve similar problems when they encounter
them ;-)




On Sat, 27 Apr 2002, [ISO-2022-JP] 矢野 雅裕 wrote:

> I have vety basic questions about modeller6v0.
> I have installed it in my PC(Linux RedHat 7).
> 
> I tried to run modeller according to manual(Tutorial on using MODELLER for
> comparative modeling).
> I can make sure Atom file,Alignment file, Script file and so on.
> 
> There is a sample script file model-default.top as follows
> (examples/tutorial-model/model-default.top).
> 
> # Homology modelling by the MODELLER TOP routine 'model'.
> 
> INCLUDE                                               # Include the
> predefined TOP routines
> 
> SET OUTPUT_CONTROL = 1 1 1 1 1      # uncomment to produce a large log file
> SET ALNFILE  = 'alignment.ali'              # alignment filename
> SET KNOWNS   = '5fd1'                        # codes of the templates
> SET SEQUENCE = '1fdx'                       # code of the target
> SET ATOM_FILES_DIRECTORY = './:../atom_files' # 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
> 
> 
> 
> According to manual
> 
> "To run MODELLER with the script file model-default.top, execute the
> following command: 
> 
>    mod model-default"
> 
> So I tried to input   mod model-default  as follows.
> 
> [root@fox08.tutorial-model] #  mod model-default
> 
> But,the answer is no directory.
> 
>  I  can't run modeller .I tried other command too.
> 
> Maybe, I don't understand very basci method.
> 
> What should I do to run modeller?
> 
>