[gmx-users] Problem with 4.0.3

[Stephen P. Molnar]

David van der Spoel wrote:
> Stephen P. Molnar wrote:
>> David van der Spoel wrote:
>>> Stephen P. Molnar wrote:
>>>> I have just downloaded and installed 4.0.3.  I received neither 
>>>> warning nor error during the process.  However when I attempt to 
>>>> run the gmxdemo I get:
>>>>
>>>> Fatal error:
>>>> Library file F.dat not found in current dir nor in default directories
>>>>
>>>> each successive step in demo gets a corresponding error message.  
>>>> Yet the 'missing' files, e.g. FF.dat are in 
>>>> /sdb5/Applications/gromacs/share/gromacs/top
>>>>
>>>> Here is what I put in my .bashrc file:
>>>>
>>>> ##########################################################
>>>> # This is the real configuration part. We save the Gromacs
>>>> # things in separate vars, so we can remove them later.
>>>> # If you move gromacs, change the next four line.
>>>> ##########################################################
>>>> GMXBIN=/sdb5/Applications/gromacs/bin
>>>> GMXLDLIB=/sdb5/Applications/gromacs/lib
>>>> GMXMAN=/sdb5/Applications/gromacs/share/man
>>>> GMXDATA=/sdb5/Applications/gromacs/share
>>>>   # NB: The variables already begin with ':' now, or are empty
>>>> LD_LIBRARY_PATH=${GMXLDLIB}${LD_LIBRARY_PATH}
>>>> PATH=${GMXBIN}${PATH}
>>>> MANPATH=${GMXMAN}${MANPATH}
>>>
>>> Try:
>>>
>>> . /sdb5/Applications/gromacs/bin/GMXRC
>>>
>>>
>>>>
>>>> # export should be separate, so /bin/sh understands it
>>>> export GMXBIN GMXLDLIB GMXMAN GMXDATA LD_LIBRARY_PATH PATH MANPATH
>>>>
>>>> Obviously I've installed gromacs in a non-default location.  What 
>>>> modifications should I make, I presume to .cashrc, so that the 
>>>> necessary files will be found?
>>>>
>>>> Thanks in advance.
>>>>
>>>> -- 
>>>> Stephen P. Molnar, Ph.D.        Life is a fuzzy set
>>>> Foundation for Chemistry        Stochastic and multivariate
>>>> http://www.geocities.com/FoundationForChemistry
>>>>
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>>>
>>>
>> Thanks for the suggestion.  Here is the result:
>>
>> computation at abnormal:/sdb5/Applications/gromacs/share/gromacs/tutor/gmxdemo> 
>> /sdb5/Applications/gromacs/bin/GMXRC
>> /sdb5/Applications/gromacs/bin/GMXRC: line 35: return: can only 
>> `return' from a function or sourced script
>> /sdb5/Applications/gromacs/bin/GMXRC: line 44: CSH:: command not found
>> /sdb5/Applications/gromacs/bin/GMXRC.csh: line 8: syntax error near 
>> unexpected token `setenv'
>> /sdb5/Applications/gromacs/bin/GMXRC.csh: line 8: `if (! 
>> $?LD_LIBRARY_PATH) setenv LD_LIBRARY_PATH ""'
>> computation at abnormal:/sdb5/Applications/gromacs/share/gromacs/tutor/gmxdemo> 
>>
>>
> You forgot the leading period ( . )
>
That is what I classify as a red faced forehead slapper.

Many thanks.  All is now well.

-- 

--
Stephen P. Molnar, Ph.D.		Life is a fuzzy set
Foundation for Chemistry		Stochastic and multivariate
http://www.geocities.com/FoundationForChemistry