[gmx-users] DSSP error

[ahmet yıldırım]

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.

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>

>
>
> 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>>
>>
>>
>>    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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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-- 
Ahmet YILDIRIM
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