[gmx-users] where does the gromacs looks for the top data file.
Justin A. Lemkul
jalemkul at vt.edu
Mon Mar 7 16:28:17 CET 2011
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:
> I got another question about where does the gromacs looks for
> the top data file.
> 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
> 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 =
> 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.
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:
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
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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