ZHAO Lina wrote:
On Mon, Mar 7, 2011 at 11:11 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@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@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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