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

[Justin A. Lemkul]

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 GROMACS
> 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.

-Justin

> Thanks,
> 
> lina
> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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