Hi, My heteromolecule structure is missing hydrogens. I did an aminoacids.hdb entry which I suppose being right. When running `g_protonate -s conf.pdb -o prot.pdb` to add the hydrogens happens an segmentation fault. The traceback for 4.6.4-dev-20130808-afc6131 follows. I could add them by any other ways, but g_protonate seems the right way to do. Can you help me to use g_protonate?
Program received signal SIGSEGV, Segmentation fault. 0x00007ffff7b22450 in calc_all_pos (pdba=0x619d20, x=0x61c6a0, nab=0x61c310, ab=0x61f9e0, bCheckMissing=0) at /home/peu/Downloads/gromacs/src/kernel/genhydro.c:392 392 if (ab[i][j].oname == NULL && ab[i][j].tp > 0) (gdb) bt #0 0x00007ffff7b22450 in calc_all_pos (pdba=0x619d20, x=0x61c6a0, nab=0x61c310, ab=0x61f9e0, bCheckMissing=0) at /home/peu/Downloads/gromacs/src/kernel/genhydro.c:392 #1 0x00007ffff7b22cd7 in add_h_low (pdbaptr=0x7fffffffc1e8, xptr=0x7fffffffced8, nah=50, ah=0x613370, nterpairs=1, ntdb=0x616440, ctdb=0x619cc0, rN=0x619ce0, rC=0x619d00, bCheckMissing=0, nabptr=0x7fffffffdf40, abptr=0x7fffffffdf48, bUpdate_pdba=1, bKeep_old_pdba=1) at /home/peu/Downloads/gromacs/src/kernel/genhydro.c:540 #2 0x00007ffff7b23b66 in add_h (pdbaptr=0x7fffffffc1e8, xptr=0x7fffffffced8, nah=50, ah=0x613370, nterpairs=1, ntdb=0x616440, ctdb=0x619cc0, rN=0x619ce0, rC=0x619d00, bAllowMissing=1, nabptr=0x7fffffffdf40, abptr=0x7fffffffdf48, bUpdate_pdba=1, bKeep_old_pdba=1) at /home/peu/Downloads/gromacs/src/kernel/genhydro.c:781 #3 0x00007ffff7b24080 in protonate (atomsptr=0x7fffffffceb8, xptr=0x7fffffffced8, protdata=0x7fffffffdf30) at /home/peu/Downloads/gromacs/src/kernel/genhydro.c:894 #4 0x00000000004020ff in cmain (argc=1, argv=0x7fffffffe0d8) at /home/peu/Downloads/gromacs/src/kernel/g_protonate.c:195 #5 0x000000000040224c in main (argc=5, argv=0x7fffffffe0d8) at /home/peu/Downloads/gromacs/src/kernel/main.c:29 abraços, Pedro Lacerda -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists