[gmx-users] g_helix segmentation fault grom-4.6.5

[Mark Abraham]

Software has bugs, unfortunately, and GROMACS tools particularly so. We are
trying to improve the situation, but if a developer isn't using a tool, it
doesn't get any love! Are you trying to say it doesn't work in 4.6.5?

Mark
On Jan 16, 2014 5:51 AM, "tarak karmakar" <tarak20489 at gmail.com> wrote:

> Dear All,
>
> Bit confused with the g_helix utility in gromacs-4.6.5.
> I've simulated a membrane protein for 50 ns in gromacs-4.5.5. Now, I'm
> trying to analyze properties of each of the trans-membrane helices. g_helix
> in gromacs-4.5.5 seems not working properly and then I moved to
> gromacs-4.6.5 tools to analyze the trajectories. While doing so,
>
> ............................................................................................
> make_ndx -f topol.tpr -o TM_1.ndx
>
> g_helix -s topol.tpr -f traj.xtc -n TM_1.ndx
>
> ...............................................................................................
> for few of the helices, it is showing
>
> ...............................................................................................
> There are 28 residues
> There are 26 complete backbone residues (from 2 to 27)
> nall=460
> Reading file topol.tpr, VERSION 4.5.5 (single precision)
> helix from: 6 through 23
> t=0.00
> Back Off! I just backed up zconf.gro to ./#zconf.gro.4#
> Segmentation fault (core dumped)
>
> ..............................................................................................
> However, for other helices the similar protocol is working perfectly fine.
> It would be highly appreciated if anyone can comment or suggest on this
> problem.
>
> regards,
> Tarak
> --
> 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-request at gromacs.org.
>