I found that with an older version g_chi works fine for the system. Thanks for your help.
On Thu, Aug 27, 2015 at 9:15 PM, Dina Mirijanian <dmi...@brandeis.edu> wrote: > No. I have ARG and LYS residues. And I checked the protein trajectory > after trjconv and these residues seemed to be whole. > > > On Thursday, August 27, 2015, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 8/27/15 12:33 PM, Dina Mirijanian wrote: >> >>> Hello, >>> >>> I have done a simulation of two protein segments in water and ions. I >>> have >>> processed my trajectory from the simulation with trjconv using the flag >>> "-pbc whole" in order to make all the bonds whole again, lets call the >>> output trajectory from this "prot_whole.xtc". >>> >>> I then run "g_chi -s protein_whole.pdb -f prot_whole.xtc -all -maxchi 6" >>> to get the files with all the dihedrals. I get the following writeout >>> before it crashes: >>> 257 residues with dihedrals found >>> 1184 dihedrals found >>> Reading frame 13000 time 325000.000 >>> Segmentation fault (core dumped) >>> >>> However when I run the same g_chi command line with -maxchi 1 it runs >>> fine >>> and writes out the .xvg files with the dihedrals: >>> 257 residues with dihedrals found >>> 1184 dihedrals found >>> Reading frame 13000 time 325000.000 >>> j after resetting (nr. active dihedrals) = 983 >>> Printing chi1VAL20.xvg >>> >>> The g_chi command works fine for -maxchi 1,2,3 but gives a Segmentation >>> fault for -maxchi 4,5,6. >>> >>> I'm having a hard time figuring out what the problem is. Has anyone ever >>> run into this problem? >>> I am using gromacs 5.0.5 >>> >>> >> Probably your structure doesn't have any residues with >3 chi torsions. >> >> -Justin >> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Ruth L. Kirschstein NRSA Postdoctoral Fellow >> >> Department of Pharmaceutical Sciences >> School of Pharmacy >> Health Sciences Facility II, Room 629 >> University of Maryland, Baltimore >> 20 Penn St. >> Baltimore, MD 21201 >> >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >> http://mackerell.umaryland.edu/~jalemkul >> >> ================================================== >> -- >> 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.