On 10/11/13 1:34 AM, Mass wrote:
Dear Mark,
Thanks for your comments, I uninstalled my previous Gromacs version ( from
Ubuntu software centre I just removed it) . and followed the dirty and quick
installation on Gromacs website
tar xfz gromacs-4.6.3.tar.gz
cd gromacs-4.6.3
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON
make
sudo make install
source /usr/local/gromacs/bin/GMXRC
I have one question here, why when I run mdrun in my home directory it is
telling me that Gromacs is not installed, but when I source it again and go to
my home directory after that mdrun show Gromacs version-4.6.3. any comments on
this? how can I call gromacs without sourcing every time
Configure your login scripts to do it for you.
secondly when I do do_dssp
do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc
Secondary_Structure_analysis_original_dss.xvg -ssdump
I am getting following error
Program mdrun, VERSION 4.6.3
Source code file: /home/mass/gromacs-4.6.3/src/gmxlib/gmxfio.c, line: 524
Can not open file:
topol.tpr
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Whatever you typed above is not what you typed in the terminal (always copy and
paste!), because do_dssp is looking for topol.tpr, which is the default name for
-s. If you do not specify a particular required input, all Gromacs programs
look for default names.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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