[gmx-users] DSSP error

[Justin A. Lemkul]

ahmet yıldırım wrote:
> Dear Justin,
> 
> Finally, The problem is solved, Thank you very much for your patience.
> 
> Ps: I set *root at ab-desktop:/home/ab/Desktop/dssp# export 
> DSSP=/usr/local/bin/dssp* the instead of 4.step but the do_dssp dont run 
> again.The I don't still understand why the DSSP environment variable is 
> not run.
> 

I'm confused.  You say the problem is solved, then you say that do_dssp is not 
running, but then your output below indicates that everything is fine.

If there is still a problem, please list all your commands in exact order (not 
"this instead of that").

To eliminate any sort of confusion, please stop setting the DSSP environment 
variable if your dssp binary is in /usr/local/bin.  As I keep telling you, if 
this is its location, it is exactly what Gromacs expects and you do not need it 
whatsoever.  You only need to set DSSP if your binary is in some other location.

-Justin

> Thanks again
> 
> Final solution:
> 1.step-root at ab-desktop:/home/ab/Desktop# tar xvzf dsspcmbi.tar.gz
> 2.step-root at ab-desktop:/home/ab/Desktop/dssp#./DsspCompileGCC
> 3.step-root at ab-desktop:/home/ab/Desktop/dssp# cp dsspcmbi dssp
> 4.step-root at ab-desktop:/home/ab/Desktop/dssp# mv dssp /usr/local/bin
> 5.step-ab at ab-desktop:~/Desktop/gromacswork$ do_dssp -s run.tpr -f run.xtc
> 
> Selected 1: 'Protein'
> There are 164 residues in your selected group
> Opening library file /usr/share/gromacs/top/ss.map
> Reading frame       0 time    0.000  
> Back Off! I just backed up ddqL3oYP to ./#ddqL3oYP.1#
> Last frame         50 time   10.000  
> 
> 100%
> gcq#29: "No One Could Foresee the End That Came So Fast" (Slayer)
> 
> 
> 2010/11/10 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> 
> 
> 
>     ahmet yıldırım wrote:
> 
> 
>         1.step-root at ab-desktop:/home/ab/Desktop# tar xvzf dsspcmbi.tar.gz
>         2.step-root at ab-desktop:/home/ab/Desktop/dssp#./DsspCompileGCC
>         3.step-root at ab-desktop:/home/ab/Desktop/dssp# cp dsspcmbi dssp
>         4.step-root at ab-desktop:/home/ab/Desktop/dssp# export
>         DSSP=/usr/local/bin/dssp
> 
>         Dear Justin,
>         I compiled the program. you said "Your environment variable is
>         wrong", Now is it true??
> 
> 
>     Yes, although it's still not necessary.  As I said before, if your
>     dssp binary is in /usr/local/bin/dssp, then that's what Gromacs
>     expects.  You only have to set the DSSP environment variable if
>     you've got the dssp binary somewhere else.
> 
>     -Justin
> 
>         Thanks for your helps
> 
>         2010/11/10 Ali Naqvi <mnaqvi at ryerson.ca
>         <mailto:mnaqvi at ryerson.ca> <mailto:mnaqvi at ryerson.ca
>         <mailto:mnaqvi at ryerson.ca>>>
> 
> 
>            May be the directory you are working in is read only, as Justin
>            mentioned this could be a permissions issue.
>            As an example the super computer that I use, cannot write
>         anything
>            in the home directory, therefore all simulations and analysis are
>            done in scratch.
> 
>            Ali
> 
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> 
> 
> 
>         -- 
>         Ahmet YILDIRIM
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
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> 
> 
> 
> -- 
> Ahmet YILDIRIM

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================