[gmx-users] secondary structure analysis

[Joe Jordan]

You may want to familiarize yourself with how the terminal works before
proceeding. You need to give the path on your machine for dssp.

On Wed, May 16, 2018 at 12:13 PM, SHAHEE ISLAM <islamshahee at gmail.com>
wrote:

> when i am using command
> dssp -h
> below are shown on the terminal screen
> DSSP 2.0.4 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
>   --version             Print version
>   -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
>
> but when i am trying
> dssp.exe -i 5B1F2.PDB -o 1crn.dssp
> error is
> dssp.exe: command not found
> thanking you
>
> On 5/16/18, Joe Jordan <e.jjordan12 at gmail.com> wrote:
> > Have you tried running the dssp command on a pdb file to ensure that it
> is
> > working as intended? FYI 4.5.5 is no longer supported so you may want to
> > consider upgrading to (the much faster) gromacs 2018.
> >
> > On Wed, May 16, 2018 at 11:45 AM, SHAHEE ISLAM <islamshahee at gmail.com>
> > wrote:
> >
> >> i have installed dssp2.04 in usr/local/bin.
> >>
> >> On 5/16/18, Joe Jordan <e.jjordan12 at gmail.com> wrote:
> >> > You have to point to where you have dssp installed. This may require
> >> > you
> >> to
> >> > install dssp.
> >> >
> >> > On Wed, May 16, 2018 at 11:41 AM, SHAHEE ISLAM <islamshahee at gmail.com
> >
> >> > wrote:
> >> >
> >> >> i want calculate the secondary structure of protein in gromacs.but
> >> >> when i am using this command
> >> >>
> >> >> do_dssp -f dynamic.xtc -s dynamic.tpr -sc scount.xvg -o ss.xpm -dt 10
> >> >>
> >> >> getting this error
> >> >> Program do_dssp, VERSION 4.5.5
> >> >> Source code file: /build/buildd/gromacs-4.5.5/src/tools/do_dssp.c,
> >> line:
> >> >> 572
> >> >>
> >> >> Fatal error:
> >> >> Failed to execute command: /usr/local/bin/dssp -na ddsbJ3bY ddT7Ubn7
> >
> >> >> /dev/null 2> /dev/null
> >> >> For more information and tips for troubleshooting, please check the
> >> >> GROMACS
> >> >> website at http://www.gromacs.org/Documentation/Errors
> >> >>       how i will solve this problem.please help me
> >> >> --
> >> >> Gromacs Users mailing list
> >> >>
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> or
> >> >> send a mail to gmx-users-request at gromacs.org.
> >> >>
> >> >
> >> >
> >> >
> >> > --
> >> > Joe Jordan
> >> > --
> >> > Gromacs Users mailing list
> >> >
> >> > * Please search the archive at
> >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >> >
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> >> send a
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> >> >
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at http://www.gromacs.org/
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> >>
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> >>
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> >>
> >
> >
> >
> > --
> > Joe Jordan
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
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> send a
> > mail to gmx-users-request at gromacs.org.
> >
> --
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>
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>
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>
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>



-- 
Joe Jordan