[gmx-users] getting dssp executable

[francesca vitalini]

Thanks!
However now I jet another error
-bash: export: `/home/cocktail/vitalini/gromacs_special/bin/dssp': not
a valid identifier
even though the path is correct and I have saved the binary file that
I downloaded with the name dssp. Do you kno if after downloading I
have  to do anything with the binary file to make it work? n the dssp
website they don't write anything about it.
Thanks again



2012/2/17 Justin A. Lemkul <jalemkul at vt.edu>:
>
>
> francesca vitalini wrote:
>>
>> Dear all,
>> In order to get the secondary structure of my pdb file I need to run
>> the do_dssp program. When I try to run it however I get the following
>> error
>>
>> Program do_dssp, VERSION 3.3.1
>> Source code file: do_dssp.c, line: 448
>>
>> Fatal error:
>> DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP)
>>
>> So I went to the http://swift.cmbi.ru.nl/gv/dssp/DSSP_5.html website
>> and downloaded the program. when then I try to settle the environment
>> variable
>>
>> set an environment variable DSSP pointing to the dssp executable, e.g.:
>>
>> setenv DSSP /opt/dssp/bin/dssp
>>
>> then I get the following error message:
>>
>> -bash: setenv: command not found
>>
>
> You need to use "export" for bash; "setenv" is for csh.
>
> export DSSP=/opt/dssp/bin/dssp
>
> -Justin
>
> --
> ========================================
>
> 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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-- 
Francesca Vitalini

PhD student at Computational Molecular Biology Group,
Department of Mathematics and Informatics, FU-Berlin
Arnimallee 6 14195 Berlin

vitalini at zedat.fu-berlin.de
francesca.vitalini at fu-berlin.de

+49 3083875776
+49 3083875412