[gmx-users] segmentation fault on g_protonate

[Justin Lemkul]

On 8/9/13 2:35 PM, Pedro Lacerda wrote:
> 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
>

Please file a bug report on redmine.gromacs.org.  g_protonate has been in 
varying states of disrepair for years.  I hacked a fix a long time ago, but 
apparently something has broken again.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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