[gmx-users] DSSP installation on Ubuntu 12.10

Mass masstransfer_2010 at yahoo.com
Fri Oct 11 07:34:05 CEST 2013

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
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 

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:
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

any comments?  

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