[gmx-users] getting dssp executable

[francesca vitalini]

Thanks. I was mislead by the syntax in the online reference and forgot
to change everything into bash scripting.
You have been very very helpful!


2012/2/17 Justin A. Lemkul <jalemkul at vt.edu>:
>
>
> francesca vitalini wrote:
>>
>> export DSSP /home/cocktail/vitalini/gromacs_special/bin/dssp
>>
>
> You forgot an '=' sign in the variable assignment.
>
> export DSSP=/home/...
>
> -Justin
>
>
>> 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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>>
>>
>>
>>
>
> --
> ========================================
>
> 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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-- 
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