[gmx-users] Operation of tutorial

[Itamar Kass]

Good morning Joe, this is due to the fact the osX does not recognize 
the links.  In order to over come it you should use the command's full 
path (e.g. /usr/local/gromacs/.../bin/pdb2gmx).

On Dec 3, 2004, at 11:59 PM, Oliver Beckstein wrote:

> Hi Joe,
>
> I am not using MacOS myself but perhaps it's more a simple
> shell/environment problem.
>
>> I am now working through the tutorials and have hit a second snag, in 
>> that
>> my computer is not recognizing the commands ³demo² or ³pdb2gmx². I 
>> have
>> successfully configured and installed both fftw and gromacs.  Upon
>> installation, the program placed the /bin file (which contains 
>> pdb2gmx)
>> inside of another directory, powerpc-apple-darwin7.6.0. I tried 
>> setting the
>> path in two ways using the setenv command described in the online
>> documentation, first as (in my case) /Users/jbozell/gromacs/bin, and 
>> then as
>> /Users/jbozell/gromacs/ powerpc-apple-darwin7.6.0/bin.  In both 
>> cases, when
>
>
> If you installed gromacs with the canonical 'make install' then you 
> should
> also have a file .../gromacs/powerpc-apple-darwin7.6.0/bin/GMXRC
> Then you should be able to setup the Gromacs environment by sourcing 
> it,
> ie
>
>   source .../gromacs/powerpc-apple-darwin7.6.0/bin/GMXRC
>
> (where ... = ~ or /Users/jbozell or whereever you installed it). This
> should also set paths to libraries, eg check with 'echo $GMXDATA'. In
> particular, it adds the bin directory to your PATH. You should now be 
> able
> to execute all gmx programs; check with
>
>   pdb2gmx -h
>
> For problems with demo I'm just guessing that perhaps the current
> directory '.' is not in your PATH and then you'd need to execute 
> './demo'
> instead of 'demo'.
>
>
>> I moved to the directory containing the first demo, entering ³demo² 
>> resulted
>> in the reply ³command not found².  I have also copied the bin file 
>> from its
>> initial location into the gromacs file and reset the path as
>> /Users/jbozell/gromacs/bin.  Again, the command is not recognized. I 
>> get the
>> same result from entering pdb2gmx.
>
> (I my comments above I assumed that the directoryt layout is the one
> after the initial installation.) Btw, you can have a look at GMXRC and
> GMXRC.csh (and the others) to find out where the Gromacs installation
> procedure beliefs your files to be located.
>
> Oli
>
> -- 
> Oliver Beckstein * oliver at biop.ox.ac.uk
>  http://sansom.biop.ox.ac.uk/oliver/
>
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