[gmx-users] DSSP installation on Ubuntu 12.10

[Mark Abraham]

Maintaining your login scripts is a basic UNIX issue, not a GROMACS issue.
Google knows a lot more about it than anybody here ;-)

Mark


On Fri, Oct 11, 2013 at 2:57 PM, Mass <masstransfer_2010 at yahoo.com> wrote:

> Dear Gromacs user,
> Can anyone tell me how  to arrange for my login scripts to source gromacs
> automatically? Justin just point that to me and in Gromacs website it is
> written search the web for that, anyone know how to do that?
> Thanks
>
>
>
> On Saturday, October 12, 2013 1:12 AM, Mass <masstransfer_2010 at yahoo.com>
> wrote:
>
> Hi Justin,
> Sorry for the mistake,
> I typed in terminal
> do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc
> Secondary_Structure_analysis_original_dss.xvg -ssdump
>
>
> and got the following error,
>
> Program do_dssp, VERSION 4.6.3
> Source code file: /home/mass/gromacs-4.6.3/src/gmxlib/gmxfio.c, line: 524
>
> Can not open file:
> bLac_orig_md2.trr
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> I can see the file bLac_orig_md2.trr in the directory
>
> any comments?
>
>
>
> On Saturday, October 12, 2013 12:55 AM, Justin Lemkul <jalemkul at vt.edu>
> wrote:
>
>
>
> 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
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
>
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