[gmx-users] DSSP

[João Henriques]

There's no DSSP version 3 that I know of. That can't be right.

J

On Tue, Dec 5, 2017 at 5:52 PM, Vidya R <vidyadevi2811 at gmail.com> wrote:

> Hi,
>
> I have installed dssp version
>
>
> *3.0.0-win32*
>
> *What should be the command now?*
>
> On Tue, Dec 5, 2017 at 10:08 PM, João Henriques <
> joao.m.a.henriques at gmail.com> wrote:
>
> > Did you specify the DSSP version as the error message suggests? DSSP
> > version 2 has different syntax from the previous one. On the gromacs
> 5.1.4
> > do_dssp assumes that you're using version 2, but maybe yours is version
> 1.
> >
> > P.S.: I am assuming you have done everything else correctly, i.e., you
> have
> > a working DSSP executable and you have exported that executable path as
> > $DSSP.
> >
> > J
> >
> > On Tue, Dec 5, 2017 at 3:41 PM, Vidya R <vidyadevi2811 at gmail.com> wrote:
> >
> > > I got the error
> > >
> > > dssp cmd='/usr/local/bin -i ddpEbgmY -o ddtFRo32 > /dev/null 2>
> > /dev/null'
> > > Reading frame       0 time    0.000
> > > Back Off! I just backed up ddpEbgmY to ./#ddpEbgmY.1#
> > >
> > > -------------------------------------------------------
> > > Program gmx do_dssp, VERSION 5.1.4
> > > Source code file:
> > > /cygdrive/d/software/GROMACS/gromacs-5.1.4/src/gromacs/gmxana/
> > >
> > > gmx_do_dssp.c, line: 663
> > >
> > > Fatal error:
> > > Failed to execute command: Try specifying your dssp version with the
> -ver
> > > option                                                          .
> > >
> > > For more information and tips for troubleshooting, please check the
> > GROMACS
> > > website at http://www.gromacs.org/Documentation/Errors
> > >
> > >
> > > On Tue, Dec 5, 2017 at 6:36 PM, João Henriques <
> > > joao.m.a.henriques at gmail.com
> > > > wrote:
> > >
> > > > Hi!
> > > >
> > > > This is not so much for you as it is for the other users and
> > developers.
> > > I
> > > > think I found a problem with the DSSP code when compiling using the
> > > latest
> > > > boost version (1.65.1). "tr1/tuple.hpp" cannot be found within the
> > > > "include" directory of this new boost, and the compilation fails. The
> > > error
> > > > is reproducible if you instead use homebrew to install DSSP.
> > > >
> > > > I've emailed Maarten at "m.hekkelman at cmbi.ru.nl" but I'm not sure
> this
> > > > email is active anymore. Hopefully it is, otherwise please let me
> know.
> > > >
> > > > Best regards,
> > > > J
> > > >
> > > > On Tue, Dec 5, 2017 at 6:38 AM, Vidya R <vidyadevi2811 at gmail.com>
> > wrote:
> > > >
> > > > > Hi gromacs users,
> > > > >
> > > > > I use gromacs 5.1.4 in *cygwin* (OS windows 7, 64 bit.)
> > > > >
> > > > > I want to download and install dssp tool.
> > > > >
> > > > > How to proceed?
> > > > >
> > > > >
> > > > > Thanks,
> > > > > Vidya.R
> > > > > --
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