[gmx-users] segmentation fault on g_protonate

[Pedro Lacerda]

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