[gmx-users] getting dssp executable

[francesca vitalini]

export DSSP /home/cocktail/vitalini/gromacs_special/bin/dssp

2012/2/17 Justin A. Lemkul <jalemkul at vt.edu>:
>
>
> francesca vitalini wrote:
>>
>> 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.
>
>
> What was your exact export command?
>
> -Justin
>
>
>> 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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>>
>>
>>
>>
>
> --
> ========================================
>
> 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