[gmx-users] DSSP installation on Ubuntu 12.10

Justin Lemkul jalemkul at vt.edu
Fri Oct 11 13:55:46 CEST 2013

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
> 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 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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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