[gmx-users] Re: do_dssp

[bharat gupta]

Ok now after downloading the latest version of dssp, and giving right
permissions and after executing the /usr/local/bin/dssp command I am
getting the following output :-

[root at BHARATPC peptide2]# /usr/local/bin/dssp
DSSP options:
  -h [ --help ]         Display help message
  -i [ --input ] arg    Input file
  -o [ --output ] arg   Output file, use 'stdout' to output to screen
  -v [ --verbose ]      Verbose output
  -d [ --debug ] arg    Debug level (for even more verbose output)


Examples:

To calculate the secondary structure for the file 1crn.pdb and
write the result to a file called 1crn.dssp, you type:

  dssp.exe -i 1crn.pdb -o 1crn.dssp



On Thu, Apr 5, 2012 at 4:23 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  On 5/04/2012 5:16 PM, bharat gupta wrote:
>
> *This is the output  :
>
> [root at BHARATPC ~]# /usr/local/bin/dssp
> *
>
>
> Don't run as root except for installing software, unless you like
> rebuilding your computer from the ground up.
>
> *bash: /usr/local/bin/dssp: Permission denied
> *
>
>
> Possibly you didn't give execute permission on some file or other. This is
> not a GROMACS problem, but rather a problem with how you have done your
> dssp installation. Consult its documentation.
>
>
> *
> I have already set the pat for dssp in .bashrc using export command , I
> don't know why this error is there. Is it due to renaming dsspcmbi to dssp
> ??
> *
>
>
> You have now reported testing a command different from the one you
> reported that you had instructed do_dssp to use. So it is hard for me to
> believe your assertion that you are following the advice in do_dssp -h
> correctly with a correct version of DSSP.
>
>
> Mark
>
> * *
>
> On Thu, Apr 5, 2012 at 4:08 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
>
>>  On 5/04/2012 4:16 PM, bharat gupta wrote:
>>
>> Yes , I am using the correct options for dssp. But still I am getting the
>> same error.
>>
>>
>>  What does invoking /usr/local/bin/dsspcmbi say?
>>
>> Mark
>>
>>
>>
>> On Thu, Apr 5, 2012 at 2:12 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
>>
>>>  On 5/04/2012 10:25 AM, bharat gupta wrote:
>>>
>>>> Hi,
>>>>
>>>> I am trying to plot the ss content using the do_dssp command , but I am
>>>> getting the following error :-
>>>>
>>>> Failed to execute command: /usr/local/bin/dsspcmbi -na ddldj5Bn
>>>> ddXN9mH0 > /dev/null 2> /dev/null
>>>>
>>>> I am using the DSSPold version. What could be the possible reason for
>>>> such an error ??
>>>>
>>>
>>>  Many of them. Start by making sure you're following the advice of
>>> do_dssp -h.
>>>
>>> Mark
>>>
>>> --
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>>
>>
>>
>> --
>> Bharat
>> Ph.D. Candidate
>> Room No. : 7202A, 2nd Floor
>> Biomolecular Engineering Laboratory
>> Division of Chemical Engineering and Polymer Science
>> Pusan National University
>> Busan -609735
>> South Korea
>> Lab phone no. - +82-51-510-3680, +82-51-583-8343
>> Mobile no. - 010-5818-3680
>> E-mail : monu46010 at yahoo.com
>>
>>
>>
>>
>>
>> --
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>
>
>
> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46010 at yahoo.com
>
>
>
>
>
> --
> 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!
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> www interface or send it to gmx-users-request at gromacs.org.
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>



-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46010 at yahoo.com
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