[gmx-users] GROMACS 5.1.4 and dssp 2.2.1

[Joe Jordan]

You can find a dssp binary here http://swift.cmbi.ru.nl/gv/dssp/
It is also in the ubuntu repo.
You should to get mkdssp and/or dssp to work on their own and if you can't
then your problem is not with gmx.

On Tue, Mar 13, 2018 at 10:15 AM, Simon Kit Sang Chu <simoncks1994 at gmail.com
> wrote:

> Hi everyone,
>
> I linked dssp as mkdssp and it still does not work. I try to run dssp in
> terminal. This is the result.
>
> mkdssp 2.2.1 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 -i 1crn.pdb -o 1crn.dssp
>
> Hope it behaves normally.
>
> Simon
>
> 2018-03-13 17:07 GMT+08:00 Mark Abraham <mark.j.abraham at gmail.com>:
>
> > Hi,
> >
> > gmx do_dssp -h
> >
> > says everything there is to say about how to get this to work. I've no
> idea
> > what mkdssp is, but unless it does the same things as dssp, it won't
> work.
> >
> > Mark
> >
> > On Tue, Mar 13, 2018 at 9:56 AM Simon Kit Sang Chu <
> simoncks1994 at gmail.com
> > >
> > wrote:
> >
> > > Hi João,
> > >
> > > Thanks for your suggestion. Unfortunately, the error persists. I
> thought
> > > -ver 2 was the default value.
> > >
> > > Regards,
> > > Simon
> > >
> > > 2018-03-13 15:58 GMT+08:00 João Henriques <
> joao.m.a.henriques at gmail.com>
> > :
> > >
> > > > "Fatal error: Failed to execute command: Try specifying your dssp
> > version
> > > > with the -ver option."
> > > >
> > > > Did you follow the error message suggestion? With DSSP 2.2.1 you need
> > to
> > > > set "-ver 2" on your gmx do_dssp command.
> > > >
> > > > J
> > > >
> > > > On Tue, Mar 13, 2018 at 8:45 AM, Simon Kit Sang Chu <
> > > > simoncks1994 at gmail.com>
> > > > wrote:
> > > >
> > > > > Hi everyone.
> > > > >
> > > > > I am trying to run do_dssp with GROMACS 5.1.4 and dssp 2.2.1. It
> > > returned
> > > > > an error:
> > > > >
> > > > >
> > > > > Fatal error:
> > > > > Failed to execute command: Try specifying your dssp version with
> the
> > > -ver
> > > > > option.
> > > > >
> > > > >
> > > > > I can run mkdssp and it is placed in bin. Is it a compatibility
> > problem
> > > > > here?
> > > > >
> > > > > Thanks in advance.
> > > > >
> > > > > Regards.
> > > > > Simon
> > > > > --
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-- 
Joe Jordan