[gmx-users] DSSP installation on Ubuntu 12.10

[Mass]

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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