[gmx-users] DSSP error

[ahmet yıldırım]

I do not have any problem. The problem is solved.

Thank you very much

10 Kasım 2010 22:45 tarihinde Justin A. Lemkul <jalemkul at vt.edu> yazdı:

>
>
> 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
>
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
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-- 
Ahmet YILDIRIM
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