[gmx-users] Re: do_dssp

[Mark Abraham]

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 
> <mailto: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 <mailto: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
>>
>>         -- 
>>         gmx-users mailing list gmx-users at gromacs.org
>>         <mailto: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
>>         <mailto:gmx-users-request at gromacs.org>.
>>         Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>>
>>     -- 
>>     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 <mailto:monu46010 at yahoo.com>
>>
>>
>>
>
>
>     --
>     gmx-users mailing list gmx-users at gromacs.org
>     <mailto: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
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
> -- 
> 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 <mailto:monu46010 at yahoo.com>
>
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120405/054bccb8/attachment.html>