[gmx-users] dssp works fine, but do_dssp gives fatal error

[Nikunj Maheshwari]

My current Gromacs version is 4.5.5
I think using the first option will be easy and quick.


On Wed, Jun 12, 2013 at 4:41 PM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:

> You have (at least) two easy options.
>
> 1) Install old_dssp that is available through the dssp web page.
> 2) Install a newer version of gromacs than you have at the moment. What
> version do you currently use?
>
> Erik
>
> On 12 Jun 2013, at 12:56, Nikunj Maheshwari <nixcrazyforher at gmail.com>
> wrote:
>
> > Yes I checked. do_dssp has no -ver option.
> > I also found out this link
> >
> > https://gerrit.gromacs.org/#/c/687/
> >
> > but dont know how to install/use it.
> >
> > Or maybe I can install DsspOld and see?
> >
> >
> >
> > On Wed, Jun 12, 2013 at 4:15 PM, Erik Marklund <erikm at xray.bmc.uu.se>
> wrote:
> >
> >> Search again. The syntax for invoking dssp changed at some point and it
> >> took a while before do_dssp adapted to that. If your do_dssp is lacking
> the
> >> -ver option then I'm quite confident that it uses the old syntax, which
> >> doesn't work with the newer versions (v. 2.0+ I think) of dssp.
> >>
> >> Erik
> >>
> >> On 12 Jun 2013, at 11:17, Nikunj Maheshwari <nixcrazyforher at gmail.com>
> >> wrote:
> >>
> >>> Yes I did searched. But for most people, there were issues regarding
> the
> >>> path or wrong DSSP.
> >>> DSSP runs for me, but do_dssp does not.
> >>>
> >>>
> >>> On Wed, Jun 12, 2013 at 2:25 PM, Erik Marklund <erikm at xray.bmc.uu.se>
> >> wrote:
> >>>
> >>>> Hi,
> >>>>
> >>>> Search the mailing list. This problem and its solution has been
> >> repeatedly
> >>>> discussed.
> >>>>
> >>>> Erik
> >>>>
> >>>> On 12 Jun 2013, at 10:31, Nikunj Maheshwari <nixcrazyforher at gmail.com
> >
> >>>> wrote:
> >>>>
> >>>>> Dear all,
> >>>>>
> >>>>> I installed dssp (Version 2.0.4) and it works perfect on a .pdb file.
> >>>>> I am trying to use it for do_dssp command but get the following error
> >>>> each
> >>>>> time:
> >>>>>
> >>>>> "Fatal error:
> >>>>> Failed to execute command: /usr/local/bin/dssp -na ddtmi68v ddwLuK68
> >
> >>>>> /dev/null 2> /dev/null
> >>>>> "
> >>>>>
> >>>>> Is there any way to rectify it?
> >>>>>
> >>>>> Thanks.
> >>>>> Nikunj
> >>>>> --
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