[gmx-users] GROMACS 5.1.4 and dssp 2.2.1

[Simon Kit Sang Chu]

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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