[gmx-users] getting dssp executable

[Justin A. Lemkul]

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

========================================