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 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" 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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