[gmx-users] Re: do_dssp
Mark Abraham
mark.abraham at anu.edu.au
Thu Apr 5 12:19:52 CEST 2012
On 05/04/12, bharat gupta <bharat.85.monu at gmail.com> wrote:
> Ok now after downloading the latest version of dssp,
This won't work, because the latest version of DSSP is newer than any released version of GROMACS, and they made big changes. This was discussed at length on the list only yesterday... go and find that thread to see how you need to proceed.
> 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
By running this program as root, you trusted it not to have a bug that could trash your computer. There is no reason to run that risk.
Mark
>
>
> 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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> > > > --
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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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> >
> > --
> > gmx-users mailing list gmx-users 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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