ahmet yıldırım wrote:
Dear Justin,
Finally, The problem is solved, Thank you very much for your patience.
Ps: I set *r...@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-r...@ab-desktop:/home/ab/Desktop# tar xvzf dsspcmbi.tar.gz
2.step-r...@ab-desktop:/home/ab/Desktop/dssp#./DsspCompileGCC
3.step-r...@ab-desktop:/home/ab/Desktop/dssp# cp dsspcmbi dssp
4.step-r...@ab-desktop:/home/ab/Desktop/dssp# mv dssp /usr/local/bin
5.step...@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 <jalem...@vt.edu <mailto:jalem...@vt.edu>>
ahmet yıldırım wrote:
1.step-r...@ab-desktop:/home/ab/Desktop# tar xvzf dsspcmbi.tar.gz
2.step-r...@ab-desktop:/home/ab/Desktop/dssp#./DsspCompileGCC
3.step-r...@ab-desktop:/home/ab/Desktop/dssp# cp dsspcmbi dssp
4.step-r...@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 <mna...@ryerson.ca
<mailto:mna...@ryerson.ca> <mailto:mna...@ryerson.ca
<mailto:mna...@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
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========================================
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
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