[gmx-users] secondary structure analysis

[SHAHEE ISLAM]

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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>> >>
>> >
>> >
>> >
>> > --
>> > 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.
>> >
>> --
>> 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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>>
>
>
>
> --
> Joe Jordan
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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