[gmx-users] g_helix segmentation fault grom-4.6.5

Thu Jan 16 11:37:40 CET 2014

Dear Mark,
Yes. It is not working in a proper manner in gromacs-4.6.5. I was trying to
figure out by looking at the hxprops.c code in the tools section, but not
found the solutions. I tried the debug option (-db) then I've got the
following

.............................................................................................................................................................
There are 26 complete backbone residues (from 2 to 27)
nall=460
Reading file topol.tpr, VERSION 4.5.5 (single precision)
helix from: 5 through 26
nca=22, nbb=110

 AA   N  Ca   C   O     Phi     Psi      D3      D4      D5 Hx?
  2 535 537 547 548  -87.88   27.33   0.670   0.665   0.634  No
  3 549 551 569 570 -157.76  159.37   0.458   0.554   0.694  No
  4 571 573 588 589   60.19  -65.80   0.383   0.323   0.541  No
  5 590 592 608 609  -83.69  -50.35   0.319   0.311   0.525 Yes
  6 610 612 627 628  -61.56  -32.92   0.358   0.297   0.492 Yes
  7 629 633 641 642  -56.92  -44.68   0.361   0.292   0.516 Yes
  8 643 645 655 656  -65.40  -37.32   0.363   0.325   0.542 Yes
  9 657 659 674 675  -65.30  -52.94   0.313   0.304   0.526 Yes
 10 676 678 695 696  -48.48  -47.51   0.304   0.311   0.495 Yes
 11 697 699 706 707  -52.09  -45.51   0.406   0.346   0.542 Yes
 12 708 710 725 726  -66.17  -43.13   0.295   0.296   0.464 Yes
 13 727 729 744 745  -57.52  -45.45   0.376   0.287   0.493 Yes
 14 746 748 764 765  -53.31  -56.03   0.300   0.298   0.522 Yes
 15 766 768 783 784  -69.20  -36.41   0.409   0.414   0.594 Yes
 16 785 787 797 798  -75.09  -31.97   0.348   0.308   0.474 Yes
 17 799 801 804 805  -68.89  -34.13   0.383   0.297   0.447 Yes
 18 806 808 823 824  -84.18  -27.95   0.432   0.337   0.501 Yes
 19 825 827 839 840  -76.00  -38.84   0.409   0.362   0.568 Yes
 20 841 843 846 847  -84.28  -35.27   0.344   0.348   0.522 Yes
 21 848 850 860 861  -66.65  -45.63   0.338   0.291   0.481 Yes
 22 862 864 867 868  -63.88  -25.20   0.352   0.268   0.483 Yes
 23 869 871 886 887  -68.60  -50.76   0.346   0.283   0.000 Yes
 24 888 890 902 903  -70.09  -30.90   0.368   0.000   0.000 Yes
 25 904 906 921 922  -61.37  -49.95   0.000   0.000   0.000 Yes
 26 923 925 940 941  -71.41  -52.67   0.000   0.000   0.000 Yes
 27 942 944 956 957   70.42  -32.67   0.000   0.000   0.000  No

t=0.00Segmentation fault (core dumped)
...............................................................................................................................................................

regards,
Tarak

On Thu, Jan 16, 2014 at 12:36 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> 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
> > --
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