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.jjorda...@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 <
> simoncks1...@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.abra...@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 <
> > simoncks1...@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.henriq...@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 <
> > > > > simoncks1...@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
> > > > > > --
> > > > > > 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
> > > > > >
> > > > > > * For (un)subscribe requests visit
> > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_
> gmx-users
> > > or
> > > > > > send a mail to gmx-users-requ...@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
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-requ...@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
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@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
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@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
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
>
>
>
>
> --
> 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
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@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

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Reply via email to