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.
0x77b22450 in calc_all_pos (pdba=0x619d20, x=0x61c6a0,
nab=0x61c310, ab=0x61f9e0, bCheckMissing=0) at
/home/peu/Downloads/gromacs/src/kernel/genhydro.c:392
392if (ab[i][j].oname == NULL ab[i][j].tp 0)
(gdb) bt
#0 0x77b22450 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 0x77b22cd7 in add_h_low (pdbaptr=0x7fffc1e8,
xptr=0x7fffced8, nah=50, ah=0x613370, nterpairs=1, ntdb=0x616440,
ctdb=0x619cc0, rN=0x619ce0, rC=0x619d00,
bCheckMissing=0, nabptr=0x7fffdf40, abptr=0x7fffdf48,
bUpdate_pdba=1, bKeep_old_pdba=1) at
/home/peu/Downloads/gromacs/src/kernel/genhydro.c:540
#2 0x77b23b66 in add_h (pdbaptr=0x7fffc1e8,
xptr=0x7fffced8, nah=50, ah=0x613370, nterpairs=1, ntdb=0x616440,
ctdb=0x619cc0, rN=0x619ce0, rC=0x619d00,
bAllowMissing=1, nabptr=0x7fffdf40, abptr=0x7fffdf48,
bUpdate_pdba=1, bKeep_old_pdba=1) at
/home/peu/Downloads/gromacs/src/kernel/genhydro.c:781
#3 0x77b24080 in protonate (atomsptr=0x7fffceb8,
xptr=0x7fffced8, protdata=0x7fffdf30) at
/home/peu/Downloads/gromacs/src/kernel/genhydro.c:894
#4 0x004020ff in cmain (argc=1, argv=0x7fffe0d8) at
/home/peu/Downloads/gromacs/src/kernel/g_protonate.c:195
#5 0x0040224c in main (argc=5, argv=0x7fffe0d8) 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
--
==
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==
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