[gmx-users] GROMACS 5.1.4 and dssp 2.2.1

Tue Mar 13 11:03:42 CET 2018

Ok, there's quite a lot going on here. The mkdssp the OP talks about is the
default name for the executable you get upon compilation from source.
Naming it dssp makes more sense, so that's why I suggested making a link
called dssp. Either way, it shouldn't matter because if you give the right
path to mkdssp or dssp or whatever name you give it, it should work.

If the standalone execution of dssp works, the problem must be with the
export.

Please confirm that you have exported the DSSP environment variable
correctly. Type "$DSSP -h" for example. If that works, then there's no
reason for gmx do_dssp to not work.

P.S.: dssp is notoriously tricky to compile, e.g. the static flag issue. I
also recently noticed that with boost >= 1.65.1, the code gets seriously
broken and needs some major modifications (see https://pastebin.com/NiQJkjuC
).

J

On Tue, Mar 13, 2018 at 10:30 AM, Simon Kit Sang Chu <simoncks1994 at gmail.com
> wrote:

> Thank you, Joe. I re-ensure that dssp works in my case. I tried:
>
> dssp prod-protein.pdb -o test.dssp
>
> The result looks fine without error text.
>
> Simon
>
> 2018-03-13 17:24 GMT+08:00 Joe Jordan <e.jjordan12 at gmail.com>:
>
> > 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
> > --
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