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.abra...@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" <tarak20...@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-requ...@gromacs.org. > > > -- > 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-requ...@gromacs.org. > -- 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-requ...@gromacs.org.