[gmx-users] getting dssp executable

[Justin A. Lemkul]

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
>>>>
>>>> ========================================
>>>> --
>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>> interface
>>>> or send it to gmx-users-request at gromacs.org.
>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>>
>>>
>> --
>> ========================================
>>
>> 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
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www interface
>> or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> 
> 

-- 
========================================

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

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