[gmx-users] where does the gromacs looks for the top data file.

ZHAO Lina lnzhao99 at gmail.com
Mon Mar 7 16:25:09 CET 2011

On Mon, Mar 7, 2011 at 11:11 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> ZHAO Lina wrote:
>> Hi,
>> I got another question about where does the gromacs looks for the top data
>> file.
>> Specifically,
>> The ~/bin ~/lib and ~/share are under my home directory.
>> the general setting (in .bash_profile) can deal with executables (PATH)
>> and libraries (LD_LIBRARY_PATH).
>> How can I set up gromacs looking for top data files in ~/share
>> After in topol.top I put
>> ; Include forcefield parameters
>> #include "/home/lina/share/gromacs/top/gromos43a1.ff/forcefield.itp"
>> I still have following problems.
>> Program grompp, VERSION 4.5.3
>> Source code file: futil.c, line: 897
>> Fatal error:
>> Library file residuetypes.dat not found in current dir nor in default
>> directories.
>> (You can set the directories to search with the GMXLIB path variable)
>> For more information and tips for troubleshooting, please check the
>> website at http://www.gromacs.org/Documentation/Errors
> Gromacs searches first in the working directory, then in $GMXLIB, then in
> any other directories included in the .mdp file "include =
> -I/whatever/directory."
> Presumably, if you installed everything in /home/lina/, then you can source
> GMXRC in ~/bin and the environment will be configured for you.
$ source GMXRC
-bash: /home/lina/bin/GMXRC.bash: No such file or directory
[lina at pineapple scripts]$ pwd

I'm confused. I have no problem with what under ~/bin and ~/lib but
something wrong with the ~/share.

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