[gmx-users] dodssp segmentation fault SOLVED for DEBIAN
raf.ponsaerts at med.kuleuven.be
Thu Jun 14 13:57:36 CEST 2012
Indeed, I am still using Gromacs-4.5.5, downloaded from gromacs.org on
Debian GNU/Linux 6.0.5 (48-core AMD64) with kernel 3.1.1 and patched
do_dssp manually as has been done for the newer releases. Works fine
with the new dssp-2.0.4 release.
On Thu, 2012-06-14 at 13:39 +0200, Erik Marklund wrote:
> This issue has been resolved so the next official release of gromacs
> will be capacle of using the newer versions of dssp.
> 14 jun 2012 kl. 12.57 skrev Denis Kazakiewicz:
> > Wow, just did that.
> > In Debian have to use 4.5.5-2 version of Gromacs from sid
> > repository.
> > Still have to use the oldest dssp
> > http://swift.cmbi.ru.nl/gv/dssp/HTML/dsspcmbi
> > It was simply Gromacs issue with no ways around.
> > And it woks:)
> > Just wondering,
> > What are other efficient ways of analyzing secondary structure
> > instead of dssp? (novice question)
> > Good luck to everybody
> > On 14.06.2012 11:59, Denis Kazakiewicz wrote:
> > > Hello
> > > Dear Gromacs users.
> > > This is many times discussed issue, however nothing seems to work
> > > so far
> > >
> > > do_dssp returns "Segmentation fault"
> > >
> > > It is the oldest version of dssp: dsspcmbi
> > > Gromacs 4.5.5 on Debian i386
> > > I did use export DSSP=/path to dssp
> > >
> > > 1. What is possibly could be?
> > > 2. Any other efficient ways of analyzing secondary structure
> > > without do_dssp (with VMD, may be)?
> > >
> > > THANKS in advance
> > --
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> Erik Marklund, PhD
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: +46 18 471 6688 fax: +46 18 511 755
> erikm at xray.bmc.uu.se
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