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

[Justin A. Lemkul]

ZHAO Lina wrote:
> 
> 
> On Mon, Mar 7, 2011 at 11:11 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto: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 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.
> 
> 
> $ source GMXRC
> -bash: /home/lina/bin/GMXRC.bash: No such file or directory
> [lina at pineapple scripts]$ pwd
> /home/lina/src/build/gromacs-4.5.3/scripts
> 
> I'm confused. I have no problem with what under ~/bin and ~/lib but 
> something wrong with the ~/share.
> 

I was assuming you had installed Gromacs in /home/lina/.  If that is not the 
case then clearly sourcing a non-existent file will not help.  Refer to:

http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation

If your environment is configured properly, there is no need to specify long 
custom paths to your force fields.  Just use the "include" keyword in your .mdp 
files.

-Justin

> lina
> 
> 

-- 
========================================

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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