Hi all, The attached gamout file crashes when OB tries to read it. The file contains three separate molecules interacting by VDW forces. Can someone who is familiar with the kekulize code please take a look at it and see what's happening?
Thanks,
Dave
Backtrace:
Program received signal SIGSEGV, Segmentation fault.
0xb7b85fb6 in OpenBabel::OBBond::GetBeginAtom (this=0x0) at
/usr/src/openbabel/include/openbabel/bond.h:210
210 OBAtom *GetBeginAtom() { return(_bgn); }
(gdb) bt
#0 0xb7b85fb6 in OpenBabel::OBBond::GetBeginAtom (this=0x0) at
/usr/src/openbabel/include/openbabel/bond.h:210
#1 0xb7c0d6b2 in OpenBabel::OBMol::expand_kekulize (this=0xbffff484,
bond_idx=11, atomState=..., bondState=...)
at /usr/src/openbabel/src/kekulize.cpp:431
#2 0xb7c0d744 in OpenBabel::OBMol::expand_kekulize (this=0xbffff484,
bond_idx=10, atomState=..., bondState=...)
at /usr/src/openbabel/src/kekulize.cpp:438
#3 0xb7c0d744 in OpenBabel::OBMol::expand_kekulize (this=0xbffff484,
bond_idx=9, atomState=..., bondState=...)
at /usr/src/openbabel/src/kekulize.cpp:438
#4 0xb7c0d744 in OpenBabel::OBMol::expand_kekulize (this=0xbffff484,
bond_idx=8, atomState=..., bondState=...)
at /usr/src/openbabel/src/kekulize.cpp:438
#5 0xb7c0d744 in OpenBabel::OBMol::expand_kekulize (this=0xbffff484,
bond_idx=7, atomState=..., bondState=...)
at /usr/src/openbabel/src/kekulize.cpp:438
#6 0xb7c0d744 in OpenBabel::OBMol::expand_kekulize (this=0xbffff484,
bond_idx=6, atomState=..., bondState=...)
at /usr/src/openbabel/src/kekulize.cpp:438
#7 0xb7c0d744 in OpenBabel::OBMol::expand_kekulize (this=0xbffff484,
bond_idx=5, atomState=..., bondState=...)
at /usr/src/openbabel/src/kekulize.cpp:438
#8 0xb7c0d744 in OpenBabel::OBMol::expand_kekulize (this=0xbffff484,
bond_idx=4, atomState=..., bondState=...)
at /usr/src/openbabel/src/kekulize.cpp:438
#9 0xb7c0d744 in OpenBabel::OBMol::expand_kekulize (this=0xbffff484,
bond_idx=3, atomState=..., bondState=...)
at /usr/src/openbabel/src/kekulize.cpp:438
#10 0xb7c0d744 in OpenBabel::OBMol::expand_kekulize (this=0xbffff484,
bond_idx=2, atomState=..., bondState=...)
at /usr/src/openbabel/src/kekulize.cpp:438
#11 0xb7c0d744 in OpenBabel::OBMol::expand_kekulize (this=0xbffff484,
bond_idx=1, atomState=..., bondState=...)
at /usr/src/openbabel/src/kekulize.cpp:438
#12 0xb7c0d744 in OpenBabel::OBMol::expand_kekulize (this=0xbffff484,
bond_idx=0, atomState=..., bondState=...)
at /usr/src/openbabel/src/kekulize.cpp:438
#13 0xb7c0d361 in OpenBabel::OBMol::start_kekulize (this=0xbffff484,
cycle=..., electron=...) at /usr/src/openbabel/src/kekulize.cpp:356
#14 0xb7c0ce74 in OpenBabel::OBMol::NewPerceiveKekuleBonds
(this=0xbffff484) at /usr/src/openbabel/src/kekulize.cpp:276
#15 0xb7b934c5 in OpenBabel::OBBond::IsKSingle (this=0x8083f28) at
/usr/src/openbabel/src/bond.cpp:449
#16 0xb7c59070 in OpenBabel::OBMol::Kekulize (this=0xbffff484) at
/usr/src/openbabel/src/mol.cpp:2793
#17 0xb7c5defd in OpenBabel::OBMol::PerceiveBondOrders
(this=0xbffff484) at /usr/src/openbabel/src/mol.cpp:3624
#18 0xb7303cc9 in OpenBabel::GAMESSOutputFormat::ReadMolecule
(this=0xb7312a38, pOb=0xbffff484, pConv=0xbffff3c0)
at /usr/src/openbabel/src/formats/gamessformat.cpp:751
#19 0xb7c70134 in OpenBabel::OBConversion::Read (this=0xbffff3c0,
pOb=0xbffff484, pin=0xbffff194)
at /usr/src/openbabel/src/obconversion.cpp:746
#20 0x0804b2e5 in main (argc=2, argv=0xbffff644) at
/usr/src/openbabel/tools/obenergy.cpp:125
crash.gamout
Description: Binary data
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