[gmx-users] GROMACS 5.1.4 and dssp 2.2.1

[Mateusz Bieniek]

I had a similar issue with dssp which suddenly stopped working. Switching
to x86 binary worked for me.

Linux Arch

Mat

On Tue, 13 Mar 2018, 09:25 Joe Jordan, <e.jjordan12 at gmail.com> wrote:

> 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
> --
> Gromacs Users mailing list
>
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