[gmx-users] Problem with 4.0.3

[David van der Spoel]

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 ( . )

-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se