Charged Ligand
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Gaetano Calabrò
Nov 3, 2014, 10:00:14 AM11/3/14
to sire-...@googlegroups.com
Hi There,
We are trying to run quantomm on a charged ligand and we have got the following error:
"/home/common/sire_quantomm/share/Sire/scripts/quantomm.py"
Reading topology file "SYSTEMUP.top"
Reading coordinate file "SYSTEM.crd"
Building 1345 molecule(s)...
...building molecule 1000 ...
Getting space information
Read space "PeriodicBox( ( 36.8865, 33.5925, 33.0236 ) )"
...complete
SQM process error. Number of remaining attempts = 5
Printing out the last 150 lines of output...
--------------------------------------------------------
AMBER SQM VERSION 14
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
QMMM: System specified with odd number of electrons ( 143)
QMMM: but odd spin ( 1). You most likely have the charge of
QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run calculation.
SQM process error. Number of remaining attempts = 4
Printing out the last 150 lines of output...
--------------------------------------------------------
AMBER SQM VERSION 14
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
QMMM: System specified with odd number of electrons ( 143)
QMMM: but odd spin ( 1). You most likely have the charge of
QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run calculation.
SQM process error. Number of remaining attempts = 3
Printing out the last 150 lines of output...
--------------------------------------------------------
AMBER SQM VERSION 14
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
QMMM: System specified with odd number of electrons ( 143)
QMMM: but odd spin ( 1). You most likely have the charge of
QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run calculation.
SQM process error. Number of remaining attempts = 2
Printing out the last 150 lines of output...
--------------------------------------------------------
AMBER SQM VERSION 14
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
QMMM: System specified with odd number of electrons ( 143)
QMMM: but odd spin ( 1). You most likely have the charge of
QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run calculation.
SQM process error. Number of remaining attempts = 1
Printing out the last 150 lines of output...
--------------------------------------------------------
AMBER SQM VERSION 14
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
QMMM: System specified with odd number of electrons ( 143)
QMMM: but odd spin ( 1). You most likely have the charge of
QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run calculation.
SQM process error. Number of remaining attempts = 0
Printing out the last 150 lines of output...
--------------------------------------------------------
AMBER SQM VERSION 14
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
QMMM: System specified with odd number of electrons ( 143)
QMMM: but odd spin ( 1). You most likely have the charge of
QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run calculation.
Traceback (most recent call last):
File "/home/common/sire_quantomm/share/Sire/scripts/quantomm.py", line 237, in <module>
QuantumToMM.run(params)
File "/home/common/sire_quantomm/bundled/lib/python3.4/site-packages/Sire/Tools/__init__.py", line 140, in inner
retval = func()
File "/home/common/sire_quantomm/bundled/lib/python3.4/site-packages/Sire/Tools/QuantumToMM.py", line 1054, in run
(qm_system,qm_moves) = loadQMMM()
File "/home/common/sire_quantomm/bundled/lib/python3.4/site-packages/Sire/Tools/QuantumToMM.py", line 968, in loadQMMM
system = loadQMMMSystem()
File "/home/common/sire_quantomm/bundled/lib/python3.4/site-packages/Sire/Tools/QuantumToMM.py", line 732, in loadQMMMSystem
qm_intra = qm_ligand.energy().value()
UserWarning: Exception 'SireError::process_error' thrown by the thread ''.
Could not find the total energy in the SQM output!
Thrown from FILE: /home/gac/Software/Sire_Chris/source/src/libs/Squire/sqm.cpp, LINE: 702, FUNCTION: double Squire::SQM::extractEnergy(QFile&) const
__Backtrace__
( 0) /home/common/sire_quantomm/bin/../lib/libSireError.so.0 ([0x2b0a460e0185] ++0x25)
-- SireError::getBackTrace()
( 1) /home/common/sire_quantomm/bin/../lib/libSireError.so.0 ([0x2b0a460dd440] ++0x90)
-- SireError::exception::exception(QString, QString)
/home/common/sire_quantomm/bin/../lib/libSquire.so.0(+0x5bae6) [0x2b0a520eaae6]
( 3) /home/common/sire_quantomm/bin/../lib/libSquire.so.0 ([0x2b0a5214fe49] ++0x3d9)
-- Squire::SQM::extractEnergy(QFile&) const
( 4) /home/common/sire_quantomm/bin/../lib/libSquire.so.0 ([0x2b0a5215149a] ++0x77a)
-- Squire::SQM::calculateEnergy(QString const&, int) const
( 5) /home/common/sire_quantomm/bin/../lib/libSquire.so.0 ([0x2b0a5215228e] ++0x156e)
-- Squire::SQM::calculateEnergy(QString const&, int) const
( 6) /home/common/sire_quantomm/bin/../lib/libSquire.so.0 ([0x2b0a5215228e] ++0x156e)
-- Squire::SQM::calculateEnergy(QString const&, int) const
( 7) /home/common/sire_quantomm/bin/../lib/libSquire.so.0 ([0x2b0a5215228e] ++0x156e)
-- Squire::SQM::calculateEnergy(QString const&, int) const
( 8) /home/common/sire_quantomm/bin/../lib/libSquire.so.0 ([0x2b0a5215228e] ++0x156e)
-- Squire::SQM::calculateEnergy(QString const&, int) const
( 9) /home/common/sire_quantomm/bin/../lib/libSquire.so.0 ([0x2b0a5215228e] ++0x156e)
-- Squire::SQM::calculateEnergy(QString const&, int) const
( 10) /home/common/sire_quantomm/bin/../lib/libSquire.so.0 ([0x2b0a521529b6] ++0x76)
-- Squire::SQM::calculateEnergy(SireFF::detail::FFMolecules3D<Squire::QMPotential> const&, Squire::LatticeCharges const&, int) const
( 11) /home/common/sire_quantomm/bin/../lib/libSquire.so.0 ([0x2b0a5210d17c] ++0x8c)
-- Squire::QMMMElecEmbedPotential::calculateEnergy(SireFF::detail::FFMolecules3D<Squire::QMPotential> const&, SireFF::detail::FFMolecules3D<SireMM::InterCoulombPotential> const&, SireFF::ComponentEnergy<Squire::QMComponent>&, double) const
( 12) /home/common/sire_quantomm/bin/../lib/libSquire.so.0 ([0x2b0a5211cd51] ++0x41)
-- Squire::QMMMFF::recalculateEnergy()
( 13) /home/common/sire_quantomm/bin/../lib/./libSireFF.so.0 ([0x2b0a4e713eec] ++0x9c)
-- SireFF::FF::energy(SireCAS::Symbol const&)
( 14) /home/common/sire_quantomm/bin/../lib/./libSireFF.so.0 ([0x2b0a4e71422a] ++0x3a)
-- SireFF::FF::energy()
/home/common/sire_quantomm/bundled/lib/python3.4/site-packages/Sire/FF/_FF.so(+0xeedbb) [0x2b0a4efa4dbb]
( 16) /home/common/sire_quantomm/bin/../bundled/lib/libboost_python.so ([0x2b0a4a680f05] ++0x1b5)
-- boost::python::objects::function::call(_object*, _object*) const
/home/common/sire_quantomm/bin/../bundled/lib/libboost_python.so(+0x2b138) [0x2b0a4a681138]
( 18) /home/common/sire_quantomm/bin/../bundled/lib/libboost_python.so ([0x2b0a4a68a403] ++0x43)
-- boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const
/home/common/sire_quantomm/bundled/lib/python3.4/site-packages/Sire/Error/_Error.so(+0x2465) [0x2b0a4a8a8465]
( 20) /home/common/sire_quantomm/bin/../bundled/lib/libboost_python.so ([0x2b0a4a68a3e6] ++0x26)
-- boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const
/home/common/sire_quantomm/bundled/lib/python3.4/site-packages/Sire/Error/_Error.so(+0x2423) [0x2b0a4a8a8423]
( 22) /home/common/sire_quantomm/bin/../bundled/lib/libboost_python.so ([0x2b0a4a68a1e9] ++0x29)
-- boost::python::handle_exception_impl(boost::function0<void>)
/home/common/sire_quantomm/bin/../bundled/lib/libboost_python.so(+0x29964) [0x2b0a4a67f964]
( 24) /home/common/sire_quantomm/bin/../bundled/lib/libpython3.4m.so.1.0 ([0x2b0a4634e1ae] ++0x7e)
-- PyObject_Call
( 25) /home/common/sire_quantomm/bin/../bundled/lib/libpython3.4m.so.1.0 ([0x2b0a46416244] ++0x53e4)
-- PyEval_EvalFrameEx
( 26) /home/common/sire_quantomm/bin/../bundled/lib/libpython3.4m.so.1.0 ([0x2b0a46418259] ++0x73f9)
-- PyEval_EvalFrameEx
( 27) /home/common/sire_quantomm/bin/../bundled/lib/libpython3.4m.so.1.0 ([0x2b0a46418259] ++0x73f9)
-- PyEval_EvalFrameEx
( 28) /home/common/sire_quantomm/bin/../bundled/lib/libpython3.4m.so.1.0 ([0x2b0a46418259] ++0x73f9)
-- PyEval_EvalFrameEx
( 29) /home/common/sire_quantomm/bin/../bundled/lib/libpython3.4m.so.1.0 ([0x2b0a4641961c] ++0x8ac)
-- PyEval_EvalCodeEx
( 30) /home/common/sire_quantomm/bin/../bundled/lib/libpython3.4m.so.1.0 ([0x2b0a46418141] ++0x72e1)
-- PyEval_EvalFrameEx
( 31) /home/common/sire_quantomm/bin/../bundled/lib/libpython3.4m.so.1.0 ([0x2b0a4641961c] ++0x8ac)
-- PyEval_EvalCodeEx
( 32) /home/common/sire_quantomm/bin/../bundled/lib/libpython3.4m.so.1.0 ([0x2b0a464196eb] ++0x3b)
-- PyEval_EvalCode
( 33) /home/common/sire_quantomm/bin/../bundled/lib/libpython3.4m.so.1.0 ([0x2b0a46440740] ++0xd0)
-- PyRun_FileExFlags
( 34) /home/common/sire_quantomm/bin/../bundled/lib/libpython3.4m.so.1.0 ([0x2b0a46441489] ++0x119)
-- PyRun_SimpleFileExFlags
( 35) /home/common/sire_quantomm/bin/../bundled/lib/libpython3.4m.so.1.0 ([0x2b0a46459215] ++0xbe5)
-- Py_Main
quantomm() [0x40372c]
( 37) /lib/x86_64-linux-gnu/libc.so.6 ([0x2b0a47b2176d] ++0xed)
-- __libc_start_main
quantomm() [0x4045dd]
__EndTrace__
Exception 'SireError::process_error' thrown by the thread ''.
Could not find the total energy in the SQM output!
Thrown from FILE: /home/gac/Software/Sire_Chris/source/src/libs/Squire/sqm.cpp, LINE: 702, FUNCTION: double Squire::SQM::extractEnergy(QFile&) const
I have attached the system files as well. Is quantomm able to handle charged ligands or not?
Cheers,
Gaetano
We are trying to run quantomm on a charged ligand and we have got the following error:
"/home/common/sire_quantomm/share/Sire/scripts/quantomm.py"
Reading topology file "SYSTEMUP.top"
Reading coordinate file "SYSTEM.crd"
Building 1345 molecule(s)...
...building molecule 1000 ...
Getting space information
Read space "PeriodicBox( ( 36.8865, 33.5925, 33.0236 ) )"
...complete
SQM process error. Number of remaining attempts = 5
Printing out the last 150 lines of output...
--------------------------------------------------------
AMBER SQM VERSION 14
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
QMMM: System specified with odd number of electrons ( 143)
QMMM: but odd spin ( 1). You most likely have the charge of
QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run calculation.
SQM process error. Number of remaining attempts = 4
Printing out the last 150 lines of output...
--------------------------------------------------------
AMBER SQM VERSION 14
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
QMMM: System specified with odd number of electrons ( 143)
QMMM: but odd spin ( 1). You most likely have the charge of
QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run calculation.
SQM process error. Number of remaining attempts = 3
Printing out the last 150 lines of output...
--------------------------------------------------------
AMBER SQM VERSION 14
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
QMMM: System specified with odd number of electrons ( 143)
QMMM: but odd spin ( 1). You most likely have the charge of
QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run calculation.
SQM process error. Number of remaining attempts = 2
Printing out the last 150 lines of output...
--------------------------------------------------------
AMBER SQM VERSION 14
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
QMMM: System specified with odd number of electrons ( 143)
QMMM: but odd spin ( 1). You most likely have the charge of
QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run calculation.
SQM process error. Number of remaining attempts = 1
Printing out the last 150 lines of output...
--------------------------------------------------------
AMBER SQM VERSION 14
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
QMMM: System specified with odd number of electrons ( 143)
QMMM: but odd spin ( 1). You most likely have the charge of
QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run calculation.
SQM process error. Number of remaining attempts = 0
Printing out the last 150 lines of output...
--------------------------------------------------------
AMBER SQM VERSION 14
By
Ross C. Walker, Michael F. Crowley, Scott Brozell,
Tim Giese, Andreas W. Goetz,
Tai-Sung Lee and David A. Case
--------------------------------------------------------
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
QMMM: System specified with odd number of electrons ( 143)
QMMM: but odd spin ( 1). You most likely have the charge of
QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run calculation.
Traceback (most recent call last):
File "/home/common/sire_quantomm/share/Sire/scripts/quantomm.py", line 237, in <module>
QuantumToMM.run(params)
File "/home/common/sire_quantomm/bundled/lib/python3.4/site-packages/Sire/Tools/__init__.py", line 140, in inner
retval = func()
File "/home/common/sire_quantomm/bundled/lib/python3.4/site-packages/Sire/Tools/QuantumToMM.py", line 1054, in run
(qm_system,qm_moves) = loadQMMM()
File "/home/common/sire_quantomm/bundled/lib/python3.4/site-packages/Sire/Tools/QuantumToMM.py", line 968, in loadQMMM
system = loadQMMMSystem()
File "/home/common/sire_quantomm/bundled/lib/python3.4/site-packages/Sire/Tools/QuantumToMM.py", line 732, in loadQMMMSystem
qm_intra = qm_ligand.energy().value()
UserWarning: Exception 'SireError::process_error' thrown by the thread ''.
Could not find the total energy in the SQM output!
Thrown from FILE: /home/gac/Software/Sire_Chris/source/src/libs/Squire/sqm.cpp, LINE: 702, FUNCTION: double Squire::SQM::extractEnergy(QFile&) const
__Backtrace__
( 0) /home/common/sire_quantomm/bin/../lib/libSireError.so.0 ([0x2b0a460e0185] ++0x25)
-- SireError::getBackTrace()
( 1) /home/common/sire_quantomm/bin/../lib/libSireError.so.0 ([0x2b0a460dd440] ++0x90)
-- SireError::exception::exception(QString, QString)
/home/common/sire_quantomm/bin/../lib/libSquire.so.0(+0x5bae6) [0x2b0a520eaae6]
( 3) /home/common/sire_quantomm/bin/../lib/libSquire.so.0 ([0x2b0a5214fe49] ++0x3d9)
-- Squire::SQM::extractEnergy(QFile&) const
( 4) /home/common/sire_quantomm/bin/../lib/libSquire.so.0 ([0x2b0a5215149a] ++0x77a)
-- Squire::SQM::calculateEnergy(QString const&, int) const
( 5) /home/common/sire_quantomm/bin/../lib/libSquire.so.0 ([0x2b0a5215228e] ++0x156e)
-- Squire::SQM::calculateEnergy(QString const&, int) const
( 6) /home/common/sire_quantomm/bin/../lib/libSquire.so.0 ([0x2b0a5215228e] ++0x156e)
-- Squire::SQM::calculateEnergy(QString const&, int) const
( 7) /home/common/sire_quantomm/bin/../lib/libSquire.so.0 ([0x2b0a5215228e] ++0x156e)
-- Squire::SQM::calculateEnergy(QString const&, int) const
( 8) /home/common/sire_quantomm/bin/../lib/libSquire.so.0 ([0x2b0a5215228e] ++0x156e)
-- Squire::SQM::calculateEnergy(QString const&, int) const
( 9) /home/common/sire_quantomm/bin/../lib/libSquire.so.0 ([0x2b0a5215228e] ++0x156e)
-- Squire::SQM::calculateEnergy(QString const&, int) const
( 10) /home/common/sire_quantomm/bin/../lib/libSquire.so.0 ([0x2b0a521529b6] ++0x76)
-- Squire::SQM::calculateEnergy(SireFF::detail::FFMolecules3D<Squire::QMPotential> const&, Squire::LatticeCharges const&, int) const
( 11) /home/common/sire_quantomm/bin/../lib/libSquire.so.0 ([0x2b0a5210d17c] ++0x8c)
-- Squire::QMMMElecEmbedPotential::calculateEnergy(SireFF::detail::FFMolecules3D<Squire::QMPotential> const&, SireFF::detail::FFMolecules3D<SireMM::InterCoulombPotential> const&, SireFF::ComponentEnergy<Squire::QMComponent>&, double) const
( 12) /home/common/sire_quantomm/bin/../lib/libSquire.so.0 ([0x2b0a5211cd51] ++0x41)
-- Squire::QMMMFF::recalculateEnergy()
( 13) /home/common/sire_quantomm/bin/../lib/./libSireFF.so.0 ([0x2b0a4e713eec] ++0x9c)
-- SireFF::FF::energy(SireCAS::Symbol const&)
( 14) /home/common/sire_quantomm/bin/../lib/./libSireFF.so.0 ([0x2b0a4e71422a] ++0x3a)
-- SireFF::FF::energy()
/home/common/sire_quantomm/bundled/lib/python3.4/site-packages/Sire/FF/_FF.so(+0xeedbb) [0x2b0a4efa4dbb]
( 16) /home/common/sire_quantomm/bin/../bundled/lib/libboost_python.so ([0x2b0a4a680f05] ++0x1b5)
-- boost::python::objects::function::call(_object*, _object*) const
/home/common/sire_quantomm/bin/../bundled/lib/libboost_python.so(+0x2b138) [0x2b0a4a681138]
( 18) /home/common/sire_quantomm/bin/../bundled/lib/libboost_python.so ([0x2b0a4a68a403] ++0x43)
-- boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const
/home/common/sire_quantomm/bundled/lib/python3.4/site-packages/Sire/Error/_Error.so(+0x2465) [0x2b0a4a8a8465]
( 20) /home/common/sire_quantomm/bin/../bundled/lib/libboost_python.so ([0x2b0a4a68a3e6] ++0x26)
-- boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const
/home/common/sire_quantomm/bundled/lib/python3.4/site-packages/Sire/Error/_Error.so(+0x2423) [0x2b0a4a8a8423]
( 22) /home/common/sire_quantomm/bin/../bundled/lib/libboost_python.so ([0x2b0a4a68a1e9] ++0x29)
-- boost::python::handle_exception_impl(boost::function0<void>)
/home/common/sire_quantomm/bin/../bundled/lib/libboost_python.so(+0x29964) [0x2b0a4a67f964]
( 24) /home/common/sire_quantomm/bin/../bundled/lib/libpython3.4m.so.1.0 ([0x2b0a4634e1ae] ++0x7e)
-- PyObject_Call
( 25) /home/common/sire_quantomm/bin/../bundled/lib/libpython3.4m.so.1.0 ([0x2b0a46416244] ++0x53e4)
-- PyEval_EvalFrameEx
( 26) /home/common/sire_quantomm/bin/../bundled/lib/libpython3.4m.so.1.0 ([0x2b0a46418259] ++0x73f9)
-- PyEval_EvalFrameEx
( 27) /home/common/sire_quantomm/bin/../bundled/lib/libpython3.4m.so.1.0 ([0x2b0a46418259] ++0x73f9)
-- PyEval_EvalFrameEx
( 28) /home/common/sire_quantomm/bin/../bundled/lib/libpython3.4m.so.1.0 ([0x2b0a46418259] ++0x73f9)
-- PyEval_EvalFrameEx
( 29) /home/common/sire_quantomm/bin/../bundled/lib/libpython3.4m.so.1.0 ([0x2b0a4641961c] ++0x8ac)
-- PyEval_EvalCodeEx
( 30) /home/common/sire_quantomm/bin/../bundled/lib/libpython3.4m.so.1.0 ([0x2b0a46418141] ++0x72e1)
-- PyEval_EvalFrameEx
( 31) /home/common/sire_quantomm/bin/../bundled/lib/libpython3.4m.so.1.0 ([0x2b0a4641961c] ++0x8ac)
-- PyEval_EvalCodeEx
( 32) /home/common/sire_quantomm/bin/../bundled/lib/libpython3.4m.so.1.0 ([0x2b0a464196eb] ++0x3b)
-- PyEval_EvalCode
( 33) /home/common/sire_quantomm/bin/../bundled/lib/libpython3.4m.so.1.0 ([0x2b0a46440740] ++0xd0)
-- PyRun_FileExFlags
( 34) /home/common/sire_quantomm/bin/../bundled/lib/libpython3.4m.so.1.0 ([0x2b0a46441489] ++0x119)
-- PyRun_SimpleFileExFlags
( 35) /home/common/sire_quantomm/bin/../bundled/lib/libpython3.4m.so.1.0 ([0x2b0a46459215] ++0xbe5)
-- Py_Main
quantomm() [0x40372c]
( 37) /lib/x86_64-linux-gnu/libc.so.6 ([0x2b0a47b2176d] ++0xed)
-- __libc_start_main
quantomm() [0x4045dd]
__EndTrace__
Exception 'SireError::process_error' thrown by the thread ''.
Could not find the total energy in the SQM output!
Thrown from FILE: /home/gac/Software/Sire_Chris/source/src/libs/Squire/sqm.cpp, LINE: 702, FUNCTION: double Squire::SQM::extractEnergy(QFile&) const
I have attached the system files as well. Is quantomm able to handle charged ligands or not?
Cheers,
Gaetano
Christopher Woods
Nov 3, 2014, 12:08:13 PM11/3/14
to sire-...@googlegroups.com
Hi Gaetano,
Thanks - you have found a bug in the quantomm code. It was not
correctly calculating the charge of a charged ligand. The problem was
in Tools/QuantumToMM.py, and I have attached the fixed version. Just
copy this into python/Tools (if you are installing from source), or
copy this into $SIRE/bundled/lib/python3.2/site_packages/Sire/Tools
(if you just want to fix the binary version).
Cheers,
Christopher
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---------------------------------------------------------
Christopher Woods
+44 (0) 7786 264562
http://chryswoods.com
Thanks - you have found a bug in the quantomm code. It was not
correctly calculating the charge of a charged ligand. The problem was
in Tools/QuantumToMM.py, and I have attached the fixed version. Just
copy this into python/Tools (if you are installing from source), or
copy this into $SIRE/bundled/lib/python3.2/site_packages/Sire/Tools
(if you just want to fix the binary version).
Cheers,
Christopher
> You received this message because you are subscribed to the Google Groups
> "Sire Users" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to sire-users+...@googlegroups.com.
> To post to this group, send email to sire-...@googlegroups.com.
> Visit this group at http://groups.google.com/group/sire-users.
> For more options, visit https://groups.google.com/d/optout.
--
---------------------------------------------------------
Christopher Woods
+44 (0) 7786 264562
http://chryswoods.com
Riccardo Ocello
Mar 6, 2018, 6:46:08 AM3/6/18
to Sire Users
Dear Chris and Gaetano,
Is this file to be update in 2017.3 version too??
I'm running calculations on a single K+ ions in bulk water (thus a positive "charged" system) and I got this error.
According to QM/MM step3 quantomm tutorial, I'm trying to run Multiscale Monte Carlo to sample water molecule.
SQM process error. Number of remaining attempts = 5
Printing out the last 150 lines of output...
QMMM: 1 H 3.2560 6.3850 0.1070 0.4170
QMMM: 1 H 3.6160 7.3370 -0.9530 0.4170
QMMM: 8 O 5.3160 -6.0240 5.0330 -0.8340
QMMM: 1 H 5.3530 -5.7350 4.0650 0.4170
QMMM: 1 H 4.5850 -5.4670 5.4600 0.4170
QMMM: 8 O -1.6000 -4.4480 3.5570 -0.8340
QMMM: 1 H -0.9300 -4.7600 4.1850 0.4170
QMMM: 1 H -2.2610 -4.0550 4.1630 0.4170
QMMM: 8 O 5.4650 -2.0450 7.8140 -0.8340
QMMM: 1 H 5.1500 -2.0210 6.9320 0.4170
QMMM: 1 H 4.7060 -2.4370 8.3060 0.4170
QMMM: 8 O -0.9840 -5.9140 -1.1860 -0.8340
QMMM: 1 H -0.6230 -4.9990 -1.1870 0.4170
QMMM: 1 H -1.2740 -6.2590 -0.3390 0.4170
QMMM: 8 O 8.6370 -1.0100 -5.3840 -0.8340
QMMM: 1 H 7.7860 -1.3790 -5.4870 0.4170
QMMM: 1 H 8.5940 -0.0670 -5.3750 0.4170
QMMM: 8 O -3.5610 -4.8560 -2.5450 -0.8340
QMMM: 1 H -2.6900 -5.1640 -2.1630 0.4170
QMMM: 1 H -3.8790 -4.1810 -1.8840 0.4170
QMMM: 8 O 2.0760 -5.3550 3.5660 -0.8340
QMMM: 1 H 2.0000 -4.4780 3.1480 0.4170
QMMM: 1 H 1.8270 -5.1650 4.4430 0.4170
QMMM: 8 O 7.7910 2.2600 -5.2550 -0.8340
QMMM: 1 H 7.3290 3.0950 -5.3870 0.4170
QMMM: 1 H 8.0040 2.3020 -4.3720 0.4170
QMMM: 8 O 5.7420 -8.1750 -0.2260 -0.8340
QMMM: 1 H 6.6990 -8.4460 -0.2710 0.4170
QMMM: 1 H 5.2490 -8.8260 0.3710 0.4170
QMMM: 8 O -2.3060 -1.6620 6.6870 -0.8340
QMMM: 1 H -2.6770 -1.9190 7.5080 0.4170
QMMM: 1 H -3.0090 -1.5240 6.0720 0.4170
QMMM: 8 O 8.3380 0.9700 0.1190 -0.8340
QMMM: 1 H 9.0880 0.5630 0.5320 0.4170
QMMM: 1 H 8.3110 0.5910 -0.7830 0.4170
QMMM: 8 O 0.4070 -3.3510 -1.1120 -0.8340
QMMM: 1 H -0.1900 -2.7850 -0.6140 0.4170
QMMM: 1 H 1.0770 -3.5830 -0.4530 0.4170
QMMM: 8 O 1.3160 -7.7270 -2.0440 -0.8340
QMMM: 1 H 1.3910 -8.6420 -1.8490 0.4170
QMMM: 1 H 0.4230 -7.5210 -1.8190 0.4170
QMMM: 8 O 4.0360 -2.2700 -3.3560 -0.8340
QMMM: 1 H 4.3580 -2.8620 -2.6540 0.4170
QMMM: 1 H 3.8860 -1.4110 -2.8770 0.4170
QMMM: 8 O 7.8170 2.7600 -2.5780 -0.8340
QMMM: 1 H 8.1060 2.6600 -1.6120 0.4170
QMMM: 1 H 7.1600 3.4830 -2.5530 0.4170
QMMM: 8 O 7.9370 -5.3430 1.2030 -0.8340
QMMM: 1 H 7.9180 -6.0780 1.8790 0.4170
QMMM: 1 H 7.7040 -5.8270 0.4150 0.4170
QMMM: 8 O -1.1000 -2.6900 1.2900 -0.8340
QMMM: 1 H -1.2610 -3.2940 2.0780 0.4170
QMMM: 1 H -0.4450 -1.9970 1.5310 0.4170
QMMM: 8 O 8.9060 0.6850 5.0930 -0.8340
QMMM: 1 H 8.5200 1.1950 4.3830 0.4170
QMMM: 1 H 8.2730 -0.0040 5.2720 0.4170
QMMM: 8 O 7.5170 1.8580 3.0100 -0.8340
QMMM: 1 H 7.6400 1.7730 2.0390 0.4170
QMMM: 1 H 7.2890 2.7810 3.1300 0.4170
QMMM: 8 O -0.5050 4.4160 -8.0210 -0.8340
QMMM: 1 H 0.3540 4.2030 -8.4520 0.4170
QMMM: 1 H -0.8350 3.5660 -7.9010 0.4170
QMMM: 8 O 4.6820 1.3340 4.3880 -0.8340
QMMM: 1 H 5.2360 1.9410 3.8760 0.4170
QMMM: 1 H 4.2660 0.6830 3.7630 0.4170
QMMM: 8 O 2.4140 -0.9960 3.9090 -0.8340
QMMM: 1 H 1.5230 -1.0690 4.1840 0.4170
QMMM: 1 H 2.3750 -0.2340 3.2860 0.4170
QMMM: 8 O -2.6660 7.9730 -2.9100 -0.8340
QMMM: 1 H -2.4290 8.3900 -3.8000 0.4170
QMMM: 1 H -3.4670 7.4440 -3.1150 0.4170
QMMM: 8 O 3.9120 1.0400 7.3830 -0.8340
QMMM: 1 H 3.9130 0.9320 6.4230 0.4170
QMMM: 1 H 3.6120 1.9350 7.5180 0.4170
QMMM: 8 O 6.5080 -0.4220 -2.3190 -0.8340
QMMM: 1 H 6.2440 -0.9620 -3.0660 0.4170
QMMM: 1 H 7.3040 0.0210 -2.4840 0.4170
QMMM: 8 O -3.7450 -0.1980 -9.6360 -0.8340
QMMM: 1 H -3.0460 -0.8790 -9.3290 0.4170
QMMM: 1 H -4.5410 -0.7360 -9.8040 0.4170
QMMM: 8 O -3.8600 -6.3310 -6.2960 -0.8340
QMMM: 1 H -3.2680 -6.1630 -7.0510 0.4170
QMMM: 1 H -3.1930 -6.5920 -5.6220 0.4170
QMMM: 8 O -9.5510 -2.6340 -0.8600 -0.8340
QMMM: 1 H -9.7980 -3.5210 -0.9050 0.4170
QMMM: 1 H -9.2040 -2.4370 -1.7440 0.4170
QMMM: 8 O -4.8500 1.6850 1.9940 -0.8340
QMMM: 1 H -4.6880 2.6410 2.0200 0.4170
QMMM: 1 H -4.3860 1.4050 2.7780 0.4170
QMMM: 8 O -7.8210 3.4640 -2.8230 -0.8340
QMMM: 1 H -7.2810 4.0610 -2.2630 0.4170
QMMM: 1 H -8.3600 3.0210 -2.1570 0.4170
QMMM: 8 O -0.9840 5.6900 -0.5150 -0.8340
QMMM: 1 H -0.8420 4.7690 -0.2990 0.4170
QMMM: 1 H -1.4630 5.5540 -1.3480 0.4170
QMMM: 8 O -4.7210 -4.2450 1.4570 -0.8340
QMMM: 1 H -5.4960 -4.6670 0.9670 0.4170
QMMM: 1 H -4.4360 -5.0140 2.0190 0.4170
QMMM: 8 O -9.3250 1.5740 0.9520 -0.8340
QMMM: 1 H -8.4030 1.5460 0.5740 0.4170
QMMM: 1 H -9.7350 2.1500 0.3390 0.4170
QMMM: 8 O -2.1660 4.4080 -2.4730 -0.8340
QMMM: 1 H -2.8950 4.7170 -3.0070 0.4170
QMMM: 1 H -1.8060 3.7140 -3.0740 0.4170
QMMM: 8 O -4.3330 1.8120 9.5420 -0.8340
QMMM: 1 H -4.3530 2.7430 9.4970 0.4170
QMMM: 1 H -4.1110 1.6290 8.6180 0.4170
QMMM: 8 O -1.8440 7.5640 1.5200 -0.8340
QMMM: 1 H -1.6450 8.3450 0.9210 0.4170
QMMM: 1 H -1.6660 6.8200 0.8740 0.4170
QMMM: 8 O -7.4170 6.1230 2.0460 -0.8340
QMMM: 1 H -6.5090 6.5080 2.0590 0.4170
QMMM: 1 H -7.6880 6.3120 2.8870 0.4170
QMMM: 8 O -1.4220 -9.1680 -3.6490 -0.8340
QMMM: 1 H -2.0720 -9.4700 -4.3070 0.4170
QMMM: 1 H -1.4370 -8.1990 -3.6650 0.4170
QMMM: 8 O -2.7130 0.1720 3.8150 -0.8340
QMMM: 1 H -3.3690 -0.5270 4.0770 0.4170
QMMM: 1 H -1.8810 -0.3310 3.8520 0.4170
QMMM: 8 O -1.4390 0.9240 6.8810 -0.8340
QMMM: 1 H -2.0840 1.1880 6.2020 0.4170
QMMM: 1 H -1.6910 0.0080 7.1230 0.4170
QMMM: 8 O -2.1110 6.9970 4.3600 -0.8340
QMMM: 1 H -2.0650 7.1810 3.3580 0.4170
QMMM: 1 H -1.3980 7.5620 4.7340 0.4170
QMMM: 8 O -4.6520 5.4590 -4.0120 -0.8340
QMMM: 1 H -5.0580 6.2110 -3.5350 0.4170
QMMM: 1 H -5.0360 4.6790 -3.5780 0.4170
QMMM: 8 O -8.6880 3.5770 3.8290 -0.8340
QMMM: 1 H -8.4060 3.3500 2.9630 0.4170
QMMM: 1 H -9.0950 4.4430 3.6340 0.4170
QMMM: 8 O 3.6390 6.0980 -4.7310 -0.8340
QMMM: 1 H 4.0990 5.3940 -5.1280 0.4170
QMMM: 1 H 2.7550 5.7240 -4.6570 0.4170
QMMM: 8 O -3.9870 6.0850 -6.6740 -0.8340
QMMM: 1 H -3.9840 6.0350 -5.7080 0.4170
QMMM: 1 H -4.7510 5.5160 -6.9540 0.4170
QMMM: 8 O -8.4380 -3.4640 2.2390 -0.8340
QMMM: 1 H -9.0400 -2.7500 2.0490 0.4170
QMMM: 1 H -8.8030 -4.1730 1.5530 0.4170
QMMM: 8 O -8.6860 -0.6150 -2.8270 -0.8340
QMMM: 1 H -8.6670 -1.2940 -3.5560 0.4170
QMMM: 1 H -7.9440 -0.0470 -3.0200 0.4170
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
QMMM: System specified with odd number of electrons ( 1)
QMMM: but odd spin ( 1). You most likely have the charge of
QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run calculation.
SQM process error. Number of remaining attempts = 4
Printing out the last 150 lines of output...
QMMM: 1 H 3.2560 6.3850 0.1070 0.4170
QMMM: 1 H 3.6160 7.3370 -0.9530 0.4170
QMMM: 8 O 5.3160 -6.0240 5.0330 -0.8340
QMMM: 1 H 5.3530 -5.7350 4.0650 0.4170
QMMM: 1 H 4.5850 -5.4670 5.4600 0.4170
QMMM: 8 O -1.6000 -4.4480 3.5570 -0.8340
QMMM: 1 H -0.9300 -4.7600 4.1850 0.4170
QMMM: 1 H -2.2610 -4.0550 4.1630 0.4170
QMMM: 8 O 5.4650 -2.0450 7.8140 -0.8340
QMMM: 1 H 5.1500 -2.0210 6.9320 0.4170
QMMM: 1 H 4.7060 -2.4370 8.3060 0.4170
QMMM: 8 O -0.9840 -5.9140 -1.1860 -0.8340
QMMM: 1 H -0.6230 -4.9990 -1.1870 0.4170
QMMM: 1 H -1.2740 -6.2590 -0.3390 0.4170
QMMM: 8 O 8.6370 -1.0100 -5.3840 -0.8340
QMMM: 1 H 7.7860 -1.3790 -5.4870 0.4170
QMMM: 1 H 8.5940 -0.0670 -5.3750 0.4170
QMMM: 8 O -3.5610 -4.8560 -2.5450 -0.8340
QMMM: 1 H -2.6900 -5.1640 -2.1630 0.4170
QMMM: 1 H -3.8790 -4.1810 -1.8840 0.4170
QMMM: 8 O 2.0760 -5.3550 3.5660 -0.8340
QMMM: 1 H 2.0000 -4.4780 3.1480 0.4170
QMMM: 1 H 1.8270 -5.1650 4.4430 0.4170
QMMM: 8 O 7.7910 2.2600 -5.2550 -0.8340
QMMM: 1 H 7.3290 3.0950 -5.3870 0.4170
QMMM: 1 H 8.0040 2.3020 -4.3720 0.4170
QMMM: 8 O 5.7420 -8.1750 -0.2260 -0.8340
QMMM: 1 H 6.6990 -8.4460 -0.2710 0.4170
QMMM: 1 H 5.2490 -8.8260 0.3710 0.4170
QMMM: 8 O -2.3060 -1.6620 6.6870 -0.8340
QMMM: 1 H -2.6770 -1.9190 7.5080 0.4170
QMMM: 1 H -3.0090 -1.5240 6.0720 0.4170
QMMM: 8 O 8.3380 0.9700 0.1190 -0.8340
QMMM: 1 H 9.0880 0.5630 0.5320 0.4170
QMMM: 1 H 8.3110 0.5910 -0.7830 0.4170
QMMM: 8 O 0.4070 -3.3510 -1.1120 -0.8340
QMMM: 1 H -0.1900 -2.7850 -0.6140 0.4170
QMMM: 1 H 1.0770 -3.5830 -0.4530 0.4170
QMMM: 8 O 1.3160 -7.7270 -2.0440 -0.8340
QMMM: 1 H 1.3910 -8.6420 -1.8490 0.4170
QMMM: 1 H 0.4230 -7.5210 -1.8190 0.4170
QMMM: 8 O 4.0360 -2.2700 -3.3560 -0.8340
QMMM: 1 H 4.3580 -2.8620 -2.6540 0.4170
QMMM: 1 H 3.8860 -1.4110 -2.8770 0.4170
QMMM: 8 O 7.8170 2.7600 -2.5780 -0.8340
QMMM: 1 H 8.1060 2.6600 -1.6120 0.4170
QMMM: 1 H 7.1600 3.4830 -2.5530 0.4170
QMMM: 8 O 7.9370 -5.3430 1.2030 -0.8340
QMMM: 1 H 7.9180 -6.0780 1.8790 0.4170
QMMM: 1 H 7.7040 -5.8270 0.4150 0.4170
QMMM: 8 O -1.1000 -2.6900 1.2900 -0.8340
QMMM: 1 H -1.2610 -3.2940 2.0780 0.4170
QMMM: 1 H -0.4450 -1.9970 1.5310 0.4170
QMMM: 8 O 8.9060 0.6850 5.0930 -0.8340
QMMM: 1 H 8.5200 1.1950 4.3830 0.4170
QMMM: 1 H 8.2730 -0.0040 5.2720 0.4170
QMMM: 8 O 7.5170 1.8580 3.0100 -0.8340
QMMM: 1 H 7.6400 1.7730 2.0390 0.4170
QMMM: 1 H 7.2890 2.7810 3.1300 0.4170
QMMM: 8 O -0.5050 4.4160 -8.0210 -0.8340
QMMM: 1 H 0.3540 4.2030 -8.4520 0.4170
QMMM: 1 H -0.8350 3.5660 -7.9010 0.4170
QMMM: 8 O 4.6820 1.3340 4.3880 -0.8340
QMMM: 1 H 5.2360 1.9410 3.8760 0.4170
QMMM: 1 H 4.2660 0.6830 3.7630 0.4170
QMMM: 8 O 2.4140 -0.9960 3.9090 -0.8340
QMMM: 1 H 1.5230 -1.0690 4.1840 0.4170
QMMM: 1 H 2.3750 -0.2340 3.2860 0.4170
QMMM: 8 O -2.6660 7.9730 -2.9100 -0.8340
QMMM: 1 H -2.4290 8.3900 -3.8000 0.4170
QMMM: 1 H -3.4670 7.4440 -3.1150 0.4170
QMMM: 8 O 3.9120 1.0400 7.3830 -0.8340
QMMM: 1 H 3.9130 0.9320 6.4230 0.4170
QMMM: 1 H 3.6120 1.9350 7.5180 0.4170
QMMM: 8 O 6.5080 -0.4220 -2.3190 -0.8340
QMMM: 1 H 6.2440 -0.9620 -3.0660 0.4170
QMMM: 1 H 7.3040 0.0210 -2.4840 0.4170
QMMM: 8 O -3.7450 -0.1980 -9.6360 -0.8340
QMMM: 1 H -3.0460 -0.8790 -9.3290 0.4170
QMMM: 1 H -4.5410 -0.7360 -9.8040 0.4170
QMMM: 8 O -3.8600 -6.3310 -6.2960 -0.8340
QMMM: 1 H -3.2680 -6.1630 -7.0510 0.4170
QMMM: 1 H -3.1930 -6.5920 -5.6220 0.4170
QMMM: 8 O -9.5510 -2.6340 -0.8600 -0.8340
QMMM: 1 H -9.7980 -3.5210 -0.9050 0.4170
QMMM: 1 H -9.2040 -2.4370 -1.7440 0.4170
QMMM: 8 O -4.8500 1.6850 1.9940 -0.8340
QMMM: 1 H -4.6880 2.6410 2.0200 0.4170
QMMM: 1 H -4.3860 1.4050 2.7780 0.4170
QMMM: 8 O -7.8210 3.4640 -2.8230 -0.8340
QMMM: 1 H -7.2810 4.0610 -2.2630 0.4170
QMMM: 1 H -8.3600 3.0210 -2.1570 0.4170
QMMM: 8 O -0.9840 5.6900 -0.5150 -0.8340
QMMM: 1 H -0.8420 4.7690 -0.2990 0.4170
QMMM: 1 H -1.4630 5.5540 -1.3480 0.4170
QMMM: 8 O -4.7210 -4.2450 1.4570 -0.8340
QMMM: 1 H -5.4960 -4.6670 0.9670 0.4170
QMMM: 1 H -4.4360 -5.0140 2.0190 0.4170
QMMM: 8 O -9.3250 1.5740 0.9520 -0.8340
QMMM: 1 H -8.4030 1.5460 0.5740 0.4170
QMMM: 1 H -9.7350 2.1500 0.3390 0.4170
QMMM: 8 O -2.1660 4.4080 -2.4730 -0.8340
QMMM: 1 H -2.8950 4.7170 -3.0070 0.4170
QMMM: 1 H -1.8060 3.7140 -3.0740 0.4170
QMMM: 8 O -4.3330 1.8120 9.5420 -0.8340
QMMM: 1 H -4.3530 2.7430 9.4970 0.4170
QMMM: 1 H -4.1110 1.6290 8.6180 0.4170
QMMM: 8 O -1.8440 7.5640 1.5200 -0.8340
QMMM: 1 H -1.6450 8.3450 0.9210 0.4170
QMMM: 1 H -1.6660 6.8200 0.8740 0.4170
QMMM: 8 O -7.4170 6.1230 2.0460 -0.8340
QMMM: 1 H -6.5090 6.5080 2.0590 0.4170
QMMM: 1 H -7.6880 6.3120 2.8870 0.4170
QMMM: 8 O -1.4220 -9.1680 -3.6490 -0.8340
QMMM: 1 H -2.0720 -9.4700 -4.3070 0.4170
QMMM: 1 H -1.4370 -8.1990 -3.6650 0.4170
QMMM: 8 O -2.7130 0.1720 3.8150 -0.8340
QMMM: 1 H -3.3690 -0.5270 4.0770 0.4170
QMMM: 1 H -1.8810 -0.3310 3.8520 0.4170
QMMM: 8 O -1.4390 0.9240 6.8810 -0.8340
QMMM: 1 H -2.0840 1.1880 6.2020 0.4170
QMMM: 1 H -1.6910 0.0080 7.1230 0.4170
QMMM: 8 O -2.1110 6.9970 4.3600 -0.8340
QMMM: 1 H -2.0650 7.1810 3.3580 0.4170
QMMM: 1 H -1.3980 7.5620 4.7340 0.4170
QMMM: 8 O -4.6520 5.4590 -4.0120 -0.8340
QMMM: 1 H -5.0580 6.2110 -3.5350 0.4170
QMMM: 1 H -5.0360 4.6790 -3.5780 0.4170
QMMM: 8 O -8.6880 3.5770 3.8290 -0.8340
QMMM: 1 H -8.4060 3.3500 2.9630 0.4170
QMMM: 1 H -9.0950 4.4430 3.6340 0.4170
QMMM: 8 O 3.6390 6.0980 -4.7310 -0.8340
QMMM: 1 H 4.0990 5.3940 -5.1280 0.4170
QMMM: 1 H 2.7550 5.7240 -4.6570 0.4170
QMMM: 8 O -3.9870 6.0850 -6.6740 -0.8340
QMMM: 1 H -3.9840 6.0350 -5.7080 0.4170
QMMM: 1 H -4.7510 5.5160 -6.9540 0.4170
QMMM: 8 O -8.4380 -3.4640 2.2390 -0.8340
QMMM: 1 H -9.0400 -2.7500 2.0490 0.4170
QMMM: 1 H -8.8030 -4.1730 1.5530 0.4170
QMMM: 8 O -8.6860 -0.6150 -2.8270 -0.8340
QMMM: 1 H -8.6670 -1.2940 -3.5560 0.4170
QMMM: 1 H -7.9440 -0.0470 -3.0200 0.4170
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
QMMM: System specified with odd number of electrons ( 1)
QMMM: but odd spin ( 1). You most likely have the charge of
QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run calculation.
SQM process error. Number of remaining attempts = 3
Printing out the last 150 lines of output...
QMMM: 1 H 3.2560 6.3850 0.1070 0.4170
QMMM: 1 H 3.6160 7.3370 -0.9530 0.4170
QMMM: 8 O 5.3160 -6.0240 5.0330 -0.8340
QMMM: 1 H 5.3530 -5.7350 4.0650 0.4170
QMMM: 1 H 4.5850 -5.4670 5.4600 0.4170
QMMM: 8 O -1.6000 -4.4480 3.5570 -0.8340
QMMM: 1 H -0.9300 -4.7600 4.1850 0.4170
QMMM: 1 H -2.2610 -4.0550 4.1630 0.4170
QMMM: 8 O 5.4650 -2.0450 7.8140 -0.8340
QMMM: 1 H 5.1500 -2.0210 6.9320 0.4170
QMMM: 1 H 4.7060 -2.4370 8.3060 0.4170
QMMM: 8 O -0.9840 -5.9140 -1.1860 -0.8340
QMMM: 1 H -0.6230 -4.9990 -1.1870 0.4170
QMMM: 1 H -1.2740 -6.2590 -0.3390 0.4170
QMMM: 8 O 8.6370 -1.0100 -5.3840 -0.8340
QMMM: 1 H 7.7860 -1.3790 -5.4870 0.4170
QMMM: 1 H 8.5940 -0.0670 -5.3750 0.4170
QMMM: 8 O -3.5610 -4.8560 -2.5450 -0.8340
QMMM: 1 H -2.6900 -5.1640 -2.1630 0.4170
QMMM: 1 H -3.8790 -4.1810 -1.8840 0.4170
QMMM: 8 O 2.0760 -5.3550 3.5660 -0.8340
QMMM: 1 H 2.0000 -4.4780 3.1480 0.4170
QMMM: 1 H 1.8270 -5.1650 4.4430 0.4170
QMMM: 8 O 7.7910 2.2600 -5.2550 -0.8340
QMMM: 1 H 7.3290 3.0950 -5.3870 0.4170
QMMM: 1 H 8.0040 2.3020 -4.3720 0.4170
QMMM: 8 O 5.7420 -8.1750 -0.2260 -0.8340
QMMM: 1 H 6.6990 -8.4460 -0.2710 0.4170
QMMM: 1 H 5.2490 -8.8260 0.3710 0.4170
QMMM: 8 O -2.3060 -1.6620 6.6870 -0.8340
QMMM: 1 H -2.6770 -1.9190 7.5080 0.4170
QMMM: 1 H -3.0090 -1.5240 6.0720 0.4170
QMMM: 8 O 8.3380 0.9700 0.1190 -0.8340
QMMM: 1 H 9.0880 0.5630 0.5320 0.4170
QMMM: 1 H 8.3110 0.5910 -0.7830 0.4170
QMMM: 8 O 0.4070 -3.3510 -1.1120 -0.8340
QMMM: 1 H -0.1900 -2.7850 -0.6140 0.4170
QMMM: 1 H 1.0770 -3.5830 -0.4530 0.4170
QMMM: 8 O 1.3160 -7.7270 -2.0440 -0.8340
QMMM: 1 H 1.3910 -8.6420 -1.8490 0.4170
QMMM: 1 H 0.4230 -7.5210 -1.8190 0.4170
QMMM: 8 O 4.0360 -2.2700 -3.3560 -0.8340
QMMM: 1 H 4.3580 -2.8620 -2.6540 0.4170
QMMM: 1 H 3.8860 -1.4110 -2.8770 0.4170
QMMM: 8 O 7.8170 2.7600 -2.5780 -0.8340
QMMM: 1 H 8.1060 2.6600 -1.6120 0.4170
QMMM: 1 H 7.1600 3.4830 -2.5530 0.4170
QMMM: 8 O 7.9370 -5.3430 1.2030 -0.8340
QMMM: 1 H 7.9180 -6.0780 1.8790 0.4170
QMMM: 1 H 7.7040 -5.8270 0.4150 0.4170
QMMM: 8 O -1.1000 -2.6900 1.2900 -0.8340
QMMM: 1 H -1.2610 -3.2940 2.0780 0.4170
QMMM: 1 H -0.4450 -1.9970 1.5310 0.4170
QMMM: 8 O 8.9060 0.6850 5.0930 -0.8340
QMMM: 1 H 8.5200 1.1950 4.3830 0.4170
QMMM: 1 H 8.2730 -0.0040 5.2720 0.4170
QMMM: 8 O 7.5170 1.8580 3.0100 -0.8340
QMMM: 1 H 7.6400 1.7730 2.0390 0.4170
QMMM: 1 H 7.2890 2.7810 3.1300 0.4170
QMMM: 8 O -0.5050 4.4160 -8.0210 -0.8340
QMMM: 1 H 0.3540 4.2030 -8.4520 0.4170
QMMM: 1 H -0.8350 3.5660 -7.9010 0.4170
QMMM: 8 O 4.6820 1.3340 4.3880 -0.8340
QMMM: 1 H 5.2360 1.9410 3.8760 0.4170
QMMM: 1 H 4.2660 0.6830 3.7630 0.4170
QMMM: 8 O 2.4140 -0.9960 3.9090 -0.8340
QMMM: 1 H 1.5230 -1.0690 4.1840 0.4170
QMMM: 1 H 2.3750 -0.2340 3.2860 0.4170
QMMM: 8 O -2.6660 7.9730 -2.9100 -0.8340
QMMM: 1 H -2.4290 8.3900 -3.8000 0.4170
QMMM: 1 H -3.4670 7.4440 -3.1150 0.4170
QMMM: 8 O 3.9120 1.0400 7.3830 -0.8340
QMMM: 1 H 3.9130 0.9320 6.4230 0.4170
QMMM: 1 H 3.6120 1.9350 7.5180 0.4170
QMMM: 8 O 6.5080 -0.4220 -2.3190 -0.8340
QMMM: 1 H 6.2440 -0.9620 -3.0660 0.4170
QMMM: 1 H 7.3040 0.0210 -2.4840 0.4170
QMMM: 8 O -3.7450 -0.1980 -9.6360 -0.8340
QMMM: 1 H -3.0460 -0.8790 -9.3290 0.4170
QMMM: 1 H -4.5410 -0.7360 -9.8040 0.4170
QMMM: 8 O -3.8600 -6.3310 -6.2960 -0.8340
QMMM: 1 H -3.2680 -6.1630 -7.0510 0.4170
QMMM: 1 H -3.1930 -6.5920 -5.6220 0.4170
QMMM: 8 O -9.5510 -2.6340 -0.8600 -0.8340
QMMM: 1 H -9.7980 -3.5210 -0.9050 0.4170
QMMM: 1 H -9.2040 -2.4370 -1.7440 0.4170
QMMM: 8 O -4.8500 1.6850 1.9940 -0.8340
QMMM: 1 H -4.6880 2.6410 2.0200 0.4170
QMMM: 1 H -4.3860 1.4050 2.7780 0.4170
QMMM: 8 O -7.8210 3.4640 -2.8230 -0.8340
QMMM: 1 H -7.2810 4.0610 -2.2630 0.4170
QMMM: 1 H -8.3600 3.0210 -2.1570 0.4170
QMMM: 8 O -0.9840 5.6900 -0.5150 -0.8340
QMMM: 1 H -0.8420 4.7690 -0.2990 0.4170
QMMM: 1 H -1.4630 5.5540 -1.3480 0.4170
QMMM: 8 O -4.7210 -4.2450 1.4570 -0.8340
QMMM: 1 H -5.4960 -4.6670 0.9670 0.4170
QMMM: 1 H -4.4360 -5.0140 2.0190 0.4170
QMMM: 8 O -9.3250 1.5740 0.9520 -0.8340
QMMM: 1 H -8.4030 1.5460 0.5740 0.4170
QMMM: 1 H -9.7350 2.1500 0.3390 0.4170
QMMM: 8 O -2.1660 4.4080 -2.4730 -0.8340
QMMM: 1 H -2.8950 4.7170 -3.0070 0.4170
QMMM: 1 H -1.8060 3.7140 -3.0740 0.4170
QMMM: 8 O -4.3330 1.8120 9.5420 -0.8340
QMMM: 1 H -4.3530 2.7430 9.4970 0.4170
QMMM: 1 H -4.1110 1.6290 8.6180 0.4170
QMMM: 8 O -1.8440 7.5640 1.5200 -0.8340
QMMM: 1 H -1.6450 8.3450 0.9210 0.4170
QMMM: 1 H -1.6660 6.8200 0.8740 0.4170
QMMM: 8 O -7.4170 6.1230 2.0460 -0.8340
QMMM: 1 H -6.5090 6.5080 2.0590 0.4170
QMMM: 1 H -7.6880 6.3120 2.8870 0.4170
QMMM: 8 O -1.4220 -9.1680 -3.6490 -0.8340
QMMM: 1 H -2.0720 -9.4700 -4.3070 0.4170
QMMM: 1 H -1.4370 -8.1990 -3.6650 0.4170
QMMM: 8 O -2.7130 0.1720 3.8150 -0.8340
QMMM: 1 H -3.3690 -0.5270 4.0770 0.4170
QMMM: 1 H -1.8810 -0.3310 3.8520 0.4170
QMMM: 8 O -1.4390 0.9240 6.8810 -0.8340
QMMM: 1 H -2.0840 1.1880 6.2020 0.4170
QMMM: 1 H -1.6910 0.0080 7.1230 0.4170
QMMM: 8 O -2.1110 6.9970 4.3600 -0.8340
QMMM: 1 H -2.0650 7.1810 3.3580 0.4170
QMMM: 1 H -1.3980 7.5620 4.7340 0.4170
QMMM: 8 O -4.6520 5.4590 -4.0120 -0.8340
QMMM: 1 H -5.0580 6.2110 -3.5350 0.4170
QMMM: 1 H -5.0360 4.6790 -3.5780 0.4170
QMMM: 8 O -8.6880 3.5770 3.8290 -0.8340
QMMM: 1 H -8.4060 3.3500 2.9630 0.4170
QMMM: 1 H -9.0950 4.4430 3.6340 0.4170
QMMM: 8 O 3.6390 6.0980 -4.7310 -0.8340
QMMM: 1 H 4.0990 5.3940 -5.1280 0.4170
QMMM: 1 H 2.7550 5.7240 -4.6570 0.4170
QMMM: 8 O -3.9870 6.0850 -6.6740 -0.8340
QMMM: 1 H -3.9840 6.0350 -5.7080 0.4170
QMMM: 1 H -4.7510 5.5160 -6.9540 0.4170
QMMM: 8 O -8.4380 -3.4640 2.2390 -0.8340
QMMM: 1 H -9.0400 -2.7500 2.0490 0.4170
QMMM: 1 H -8.8030 -4.1730 1.5530 0.4170
QMMM: 8 O -8.6860 -0.6150 -2.8270 -0.8340
QMMM: 1 H -8.6670 -1.2940 -3.5560 0.4170
QMMM: 1 H -7.9440 -0.0470 -3.0200 0.4170
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
QMMM: System specified with odd number of electrons ( 1)
QMMM: but odd spin ( 1). You most likely have the charge of
QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run calculation.
SQM process error. Number of remaining attempts = 2
Printing out the last 150 lines of output...
QMMM: 1 H 3.2560 6.3850 0.1070 0.4170
QMMM: 1 H 3.6160 7.3370 -0.9530 0.4170
QMMM: 8 O 5.3160 -6.0240 5.0330 -0.8340
QMMM: 1 H 5.3530 -5.7350 4.0650 0.4170
QMMM: 1 H 4.5850 -5.4670 5.4600 0.4170
QMMM: 8 O -1.6000 -4.4480 3.5570 -0.8340
QMMM: 1 H -0.9300 -4.7600 4.1850 0.4170
QMMM: 1 H -2.2610 -4.0550 4.1630 0.4170
QMMM: 8 O 5.4650 -2.0450 7.8140 -0.8340
QMMM: 1 H 5.1500 -2.0210 6.9320 0.4170
QMMM: 1 H 4.7060 -2.4370 8.3060 0.4170
QMMM: 8 O -0.9840 -5.9140 -1.1860 -0.8340
QMMM: 1 H -0.6230 -4.9990 -1.1870 0.4170
QMMM: 1 H -1.2740 -6.2590 -0.3390 0.4170
QMMM: 8 O 8.6370 -1.0100 -5.3840 -0.8340
QMMM: 1 H 7.7860 -1.3790 -5.4870 0.4170
QMMM: 1 H 8.5940 -0.0670 -5.3750 0.4170
QMMM: 8 O -3.5610 -4.8560 -2.5450 -0.8340
QMMM: 1 H -2.6900 -5.1640 -2.1630 0.4170
QMMM: 1 H -3.8790 -4.1810 -1.8840 0.4170
QMMM: 8 O 2.0760 -5.3550 3.5660 -0.8340
QMMM: 1 H 2.0000 -4.4780 3.1480 0.4170
QMMM: 1 H 1.8270 -5.1650 4.4430 0.4170
QMMM: 8 O 7.7910 2.2600 -5.2550 -0.8340
QMMM: 1 H 7.3290 3.0950 -5.3870 0.4170
QMMM: 1 H 8.0040 2.3020 -4.3720 0.4170
QMMM: 8 O 5.7420 -8.1750 -0.2260 -0.8340
QMMM: 1 H 6.6990 -8.4460 -0.2710 0.4170
QMMM: 1 H 5.2490 -8.8260 0.3710 0.4170
QMMM: 8 O -2.3060 -1.6620 6.6870 -0.8340
QMMM: 1 H -2.6770 -1.9190 7.5080 0.4170
QMMM: 1 H -3.0090 -1.5240 6.0720 0.4170
QMMM: 8 O 8.3380 0.9700 0.1190 -0.8340
QMMM: 1 H 9.0880 0.5630 0.5320 0.4170
QMMM: 1 H 8.3110 0.5910 -0.7830 0.4170
QMMM: 8 O 0.4070 -3.3510 -1.1120 -0.8340
QMMM: 1 H -0.1900 -2.7850 -0.6140 0.4170
QMMM: 1 H 1.0770 -3.5830 -0.4530 0.4170
QMMM: 8 O 1.3160 -7.7270 -2.0440 -0.8340
QMMM: 1 H 1.3910 -8.6420 -1.8490 0.4170
QMMM: 1 H 0.4230 -7.5210 -1.8190 0.4170
QMMM: 8 O 4.0360 -2.2700 -3.3560 -0.8340
QMMM: 1 H 4.3580 -2.8620 -2.6540 0.4170
QMMM: 1 H 3.8860 -1.4110 -2.8770 0.4170
QMMM: 8 O 7.8170 2.7600 -2.5780 -0.8340
QMMM: 1 H 8.1060 2.6600 -1.6120 0.4170
QMMM: 1 H 7.1600 3.4830 -2.5530 0.4170
QMMM: 8 O 7.9370 -5.3430 1.2030 -0.8340
QMMM: 1 H 7.9180 -6.0780 1.8790 0.4170
QMMM: 1 H 7.7040 -5.8270 0.4150 0.4170
QMMM: 8 O -1.1000 -2.6900 1.2900 -0.8340
QMMM: 1 H -1.2610 -3.2940 2.0780 0.4170
QMMM: 1 H -0.4450 -1.9970 1.5310 0.4170
QMMM: 8 O 8.9060 0.6850 5.0930 -0.8340
QMMM: 1 H 8.5200 1.1950 4.3830 0.4170
QMMM: 1 H 8.2730 -0.0040 5.2720 0.4170
QMMM: 8 O 7.5170 1.8580 3.0100 -0.8340
QMMM: 1 H 7.6400 1.7730 2.0390 0.4170
QMMM: 1 H 7.2890 2.7810 3.1300 0.4170
QMMM: 8 O -0.5050 4.4160 -8.0210 -0.8340
QMMM: 1 H 0.3540 4.2030 -8.4520 0.4170
QMMM: 1 H -0.8350 3.5660 -7.9010 0.4170
QMMM: 8 O 4.6820 1.3340 4.3880 -0.8340
QMMM: 1 H 5.2360 1.9410 3.8760 0.4170
QMMM: 1 H 4.2660 0.6830 3.7630 0.4170
QMMM: 8 O 2.4140 -0.9960 3.9090 -0.8340
QMMM: 1 H 1.5230 -1.0690 4.1840 0.4170
QMMM: 1 H 2.3750 -0.2340 3.2860 0.4170
QMMM: 8 O -2.6660 7.9730 -2.9100 -0.8340
QMMM: 1 H -2.4290 8.3900 -3.8000 0.4170
QMMM: 1 H -3.4670 7.4440 -3.1150 0.4170
QMMM: 8 O 3.9120 1.0400 7.3830 -0.8340
QMMM: 1 H 3.9130 0.9320 6.4230 0.4170
QMMM: 1 H 3.6120 1.9350 7.5180 0.4170
QMMM: 8 O 6.5080 -0.4220 -2.3190 -0.8340
QMMM: 1 H 6.2440 -0.9620 -3.0660 0.4170
QMMM: 1 H 7.3040 0.0210 -2.4840 0.4170
QMMM: 8 O -3.7450 -0.1980 -9.6360 -0.8340
QMMM: 1 H -3.0460 -0.8790 -9.3290 0.4170
QMMM: 1 H -4.5410 -0.7360 -9.8040 0.4170
QMMM: 8 O -3.8600 -6.3310 -6.2960 -0.8340
QMMM: 1 H -3.2680 -6.1630 -7.0510 0.4170
QMMM: 1 H -3.1930 -6.5920 -5.6220 0.4170
QMMM: 8 O -9.5510 -2.6340 -0.8600 -0.8340
QMMM: 1 H -9.7980 -3.5210 -0.9050 0.4170
QMMM: 1 H -9.2040 -2.4370 -1.7440 0.4170
QMMM: 8 O -4.8500 1.6850 1.9940 -0.8340
QMMM: 1 H -4.6880 2.6410 2.0200 0.4170
QMMM: 1 H -4.3860 1.4050 2.7780 0.4170
QMMM: 8 O -7.8210 3.4640 -2.8230 -0.8340
QMMM: 1 H -7.2810 4.0610 -2.2630 0.4170
QMMM: 1 H -8.3600 3.0210 -2.1570 0.4170
QMMM: 8 O -0.9840 5.6900 -0.5150 -0.8340
QMMM: 1 H -0.8420 4.7690 -0.2990 0.4170
QMMM: 1 H -1.4630 5.5540 -1.3480 0.4170
QMMM: 8 O -4.7210 -4.2450 1.4570 -0.8340
QMMM: 1 H -5.4960 -4.6670 0.9670 0.4170
QMMM: 1 H -4.4360 -5.0140 2.0190 0.4170
QMMM: 8 O -9.3250 1.5740 0.9520 -0.8340
QMMM: 1 H -8.4030 1.5460 0.5740 0.4170
QMMM: 1 H -9.7350 2.1500 0.3390 0.4170
QMMM: 8 O -2.1660 4.4080 -2.4730 -0.8340
QMMM: 1 H -2.8950 4.7170 -3.0070 0.4170
QMMM: 1 H -1.8060 3.7140 -3.0740 0.4170
QMMM: 8 O -4.3330 1.8120 9.5420 -0.8340
QMMM: 1 H -4.3530 2.7430 9.4970 0.4170
QMMM: 1 H -4.1110 1.6290 8.6180 0.4170
QMMM: 8 O -1.8440 7.5640 1.5200 -0.8340
QMMM: 1 H -1.6450 8.3450 0.9210 0.4170
QMMM: 1 H -1.6660 6.8200 0.8740 0.4170
QMMM: 8 O -7.4170 6.1230 2.0460 -0.8340
QMMM: 1 H -6.5090 6.5080 2.0590 0.4170
QMMM: 1 H -7.6880 6.3120 2.8870 0.4170
QMMM: 8 O -1.4220 -9.1680 -3.6490 -0.8340
QMMM: 1 H -2.0720 -9.4700 -4.3070 0.4170
QMMM: 1 H -1.4370 -8.1990 -3.6650 0.4170
QMMM: 8 O -2.7130 0.1720 3.8150 -0.8340
QMMM: 1 H -3.3690 -0.5270 4.0770 0.4170
QMMM: 1 H -1.8810 -0.3310 3.8520 0.4170
QMMM: 8 O -1.4390 0.9240 6.8810 -0.8340
QMMM: 1 H -2.0840 1.1880 6.2020 0.4170
QMMM: 1 H -1.6910 0.0080 7.1230 0.4170
QMMM: 8 O -2.1110 6.9970 4.3600 -0.8340
QMMM: 1 H -2.0650 7.1810 3.3580 0.4170
QMMM: 1 H -1.3980 7.5620 4.7340 0.4170
QMMM: 8 O -4.6520 5.4590 -4.0120 -0.8340
QMMM: 1 H -5.0580 6.2110 -3.5350 0.4170
QMMM: 1 H -5.0360 4.6790 -3.5780 0.4170
QMMM: 8 O -8.6880 3.5770 3.8290 -0.8340
QMMM: 1 H -8.4060 3.3500 2.9630 0.4170
QMMM: 1 H -9.0950 4.4430 3.6340 0.4170
QMMM: 8 O 3.6390 6.0980 -4.7310 -0.8340
QMMM: 1 H 4.0990 5.3940 -5.1280 0.4170
QMMM: 1 H 2.7550 5.7240 -4.6570 0.4170
QMMM: 8 O -3.9870 6.0850 -6.6740 -0.8340
QMMM: 1 H -3.9840 6.0350 -5.7080 0.4170
QMMM: 1 H -4.7510 5.5160 -6.9540 0.4170
QMMM: 8 O -8.4380 -3.4640 2.2390 -0.8340
QMMM: 1 H -9.0400 -2.7500 2.0490 0.4170
QMMM: 1 H -8.8030 -4.1730 1.5530 0.4170
QMMM: 8 O -8.6860 -0.6150 -2.8270 -0.8340
QMMM: 1 H -8.6670 -1.2940 -3.5560 0.4170
QMMM: 1 H -7.9440 -0.0470 -3.0200 0.4170
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
QMMM: System specified with odd number of electrons ( 1)
QMMM: but odd spin ( 1). You most likely have the charge of
QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run calculation.
SQM process error. Number of remaining attempts = 1
Printing out the last 150 lines of output...
QMMM: 1 H 3.2560 6.3850 0.1070 0.4170
QMMM: 1 H 3.6160 7.3370 -0.9530 0.4170
QMMM: 8 O 5.3160 -6.0240 5.0330 -0.8340
QMMM: 1 H 5.3530 -5.7350 4.0650 0.4170
QMMM: 1 H 4.5850 -5.4670 5.4600 0.4170
QMMM: 8 O -1.6000 -4.4480 3.5570 -0.8340
QMMM: 1 H -0.9300 -4.7600 4.1850 0.4170
QMMM: 1 H -2.2610 -4.0550 4.1630 0.4170
QMMM: 8 O 5.4650 -2.0450 7.8140 -0.8340
QMMM: 1 H 5.1500 -2.0210 6.9320 0.4170
QMMM: 1 H 4.7060 -2.4370 8.3060 0.4170
QMMM: 8 O -0.9840 -5.9140 -1.1860 -0.8340
QMMM: 1 H -0.6230 -4.9990 -1.1870 0.4170
QMMM: 1 H -1.2740 -6.2590 -0.3390 0.4170
QMMM: 8 O 8.6370 -1.0100 -5.3840 -0.8340
QMMM: 1 H 7.7860 -1.3790 -5.4870 0.4170
QMMM: 1 H 8.5940 -0.0670 -5.3750 0.4170
QMMM: 8 O -3.5610 -4.8560 -2.5450 -0.8340
QMMM: 1 H -2.6900 -5.1640 -2.1630 0.4170
QMMM: 1 H -3.8790 -4.1810 -1.8840 0.4170
QMMM: 8 O 2.0760 -5.3550 3.5660 -0.8340
QMMM: 1 H 2.0000 -4.4780 3.1480 0.4170
QMMM: 1 H 1.8270 -5.1650 4.4430 0.4170
QMMM: 8 O 7.7910 2.2600 -5.2550 -0.8340
QMMM: 1 H 7.3290 3.0950 -5.3870 0.4170
QMMM: 1 H 8.0040 2.3020 -4.3720 0.4170
QMMM: 8 O 5.7420 -8.1750 -0.2260 -0.8340
QMMM: 1 H 6.6990 -8.4460 -0.2710 0.4170
QMMM: 1 H 5.2490 -8.8260 0.3710 0.4170
QMMM: 8 O -2.3060 -1.6620 6.6870 -0.8340
QMMM: 1 H -2.6770 -1.9190 7.5080 0.4170
QMMM: 1 H -3.0090 -1.5240 6.0720 0.4170
QMMM: 8 O 8.3380 0.9700 0.1190 -0.8340
QMMM: 1 H 9.0880 0.5630 0.5320 0.4170
QMMM: 1 H 8.3110 0.5910 -0.7830 0.4170
QMMM: 8 O 0.4070 -3.3510 -1.1120 -0.8340
QMMM: 1 H -0.1900 -2.7850 -0.6140 0.4170
QMMM: 1 H 1.0770 -3.5830 -0.4530 0.4170
QMMM: 8 O 1.3160 -7.7270 -2.0440 -0.8340
QMMM: 1 H 1.3910 -8.6420 -1.8490 0.4170
QMMM: 1 H 0.4230 -7.5210 -1.8190 0.4170
QMMM: 8 O 4.0360 -2.2700 -3.3560 -0.8340
QMMM: 1 H 4.3580 -2.8620 -2.6540 0.4170
QMMM: 1 H 3.8860 -1.4110 -2.8770 0.4170
QMMM: 8 O 7.8170 2.7600 -2.5780 -0.8340
QMMM: 1 H 8.1060 2.6600 -1.6120 0.4170
QMMM: 1 H 7.1600 3.4830 -2.5530 0.4170
QMMM: 8 O 7.9370 -5.3430 1.2030 -0.8340
QMMM: 1 H 7.9180 -6.0780 1.8790 0.4170
QMMM: 1 H 7.7040 -5.8270 0.4150 0.4170
QMMM: 8 O -1.1000 -2.6900 1.2900 -0.8340
QMMM: 1 H -1.2610 -3.2940 2.0780 0.4170
QMMM: 1 H -0.4450 -1.9970 1.5310 0.4170
QMMM: 8 O 8.9060 0.6850 5.0930 -0.8340
QMMM: 1 H 8.5200 1.1950 4.3830 0.4170
QMMM: 1 H 8.2730 -0.0040 5.2720 0.4170
QMMM: 8 O 7.5170 1.8580 3.0100 -0.8340
QMMM: 1 H 7.6400 1.7730 2.0390 0.4170
QMMM: 1 H 7.2890 2.7810 3.1300 0.4170
QMMM: 8 O -0.5050 4.4160 -8.0210 -0.8340
QMMM: 1 H 0.3540 4.2030 -8.4520 0.4170
QMMM: 1 H -0.8350 3.5660 -7.9010 0.4170
QMMM: 8 O 4.6820 1.3340 4.3880 -0.8340
QMMM: 1 H 5.2360 1.9410 3.8760 0.4170
QMMM: 1 H 4.2660 0.6830 3.7630 0.4170
QMMM: 8 O 2.4140 -0.9960 3.9090 -0.8340
QMMM: 1 H 1.5230 -1.0690 4.1840 0.4170
QMMM: 1 H 2.3750 -0.2340 3.2860 0.4170
QMMM: 8 O -2.6660 7.9730 -2.9100 -0.8340
QMMM: 1 H -2.4290 8.3900 -3.8000 0.4170
QMMM: 1 H -3.4670 7.4440 -3.1150 0.4170
QMMM: 8 O 3.9120 1.0400 7.3830 -0.8340
QMMM: 1 H 3.9130 0.9320 6.4230 0.4170
QMMM: 1 H 3.6120 1.9350 7.5180 0.4170
QMMM: 8 O 6.5080 -0.4220 -2.3190 -0.8340
QMMM: 1 H 6.2440 -0.9620 -3.0660 0.4170
QMMM: 1 H 7.3040 0.0210 -2.4840 0.4170
QMMM: 8 O -3.7450 -0.1980 -9.6360 -0.8340
QMMM: 1 H -3.0460 -0.8790 -9.3290 0.4170
QMMM: 1 H -4.5410 -0.7360 -9.8040 0.4170
QMMM: 8 O -3.8600 -6.3310 -6.2960 -0.8340
QMMM: 1 H -3.2680 -6.1630 -7.0510 0.4170
QMMM: 1 H -3.1930 -6.5920 -5.6220 0.4170
QMMM: 8 O -9.5510 -2.6340 -0.8600 -0.8340
QMMM: 1 H -9.7980 -3.5210 -0.9050 0.4170
QMMM: 1 H -9.2040 -2.4370 -1.7440 0.4170
QMMM: 8 O -4.8500 1.6850 1.9940 -0.8340
QMMM: 1 H -4.6880 2.6410 2.0200 0.4170
QMMM: 1 H -4.3860 1.4050 2.7780 0.4170
QMMM: 8 O -7.8210 3.4640 -2.8230 -0.8340
QMMM: 1 H -7.2810 4.0610 -2.2630 0.4170
QMMM: 1 H -8.3600 3.0210 -2.1570 0.4170
QMMM: 8 O -0.9840 5.6900 -0.5150 -0.8340
QMMM: 1 H -0.8420 4.7690 -0.2990 0.4170
QMMM: 1 H -1.4630 5.5540 -1.3480 0.4170
QMMM: 8 O -4.7210 -4.2450 1.4570 -0.8340
QMMM: 1 H -5.4960 -4.6670 0.9670 0.4170
QMMM: 1 H -4.4360 -5.0140 2.0190 0.4170
QMMM: 8 O -9.3250 1.5740 0.9520 -0.8340
QMMM: 1 H -8.4030 1.5460 0.5740 0.4170
QMMM: 1 H -9.7350 2.1500 0.3390 0.4170
QMMM: 8 O -2.1660 4.4080 -2.4730 -0.8340
QMMM: 1 H -2.8950 4.7170 -3.0070 0.4170
QMMM: 1 H -1.8060 3.7140 -3.0740 0.4170
QMMM: 8 O -4.3330 1.8120 9.5420 -0.8340
QMMM: 1 H -4.3530 2.7430 9.4970 0.4170
QMMM: 1 H -4.1110 1.6290 8.6180 0.4170
QMMM: 8 O -1.8440 7.5640 1.5200 -0.8340
QMMM: 1 H -1.6450 8.3450 0.9210 0.4170
QMMM: 1 H -1.6660 6.8200 0.8740 0.4170
QMMM: 8 O -7.4170 6.1230 2.0460 -0.8340
QMMM: 1 H -6.5090 6.5080 2.0590 0.4170
QMMM: 1 H -7.6880 6.3120 2.8870 0.4170
QMMM: 8 O -1.4220 -9.1680 -3.6490 -0.8340
QMMM: 1 H -2.0720 -9.4700 -4.3070 0.4170
QMMM: 1 H -1.4370 -8.1990 -3.6650 0.4170
QMMM: 8 O -2.7130 0.1720 3.8150 -0.8340
QMMM: 1 H -3.3690 -0.5270 4.0770 0.4170
QMMM: 1 H -1.8810 -0.3310 3.8520 0.4170
QMMM: 8 O -1.4390 0.9240 6.8810 -0.8340
QMMM: 1 H -2.0840 1.1880 6.2020 0.4170
QMMM: 1 H -1.6910 0.0080 7.1230 0.4170
QMMM: 8 O -2.1110 6.9970 4.3600 -0.8340
QMMM: 1 H -2.0650 7.1810 3.3580 0.4170
QMMM: 1 H -1.3980 7.5620 4.7340 0.4170
QMMM: 8 O -4.6520 5.4590 -4.0120 -0.8340
QMMM: 1 H -5.0580 6.2110 -3.5350 0.4170
QMMM: 1 H -5.0360 4.6790 -3.5780 0.4170
QMMM: 8 O -8.6880 3.5770 3.8290 -0.8340
QMMM: 1 H -8.4060 3.3500 2.9630 0.4170
QMMM: 1 H -9.0950 4.4430 3.6340 0.4170
QMMM: 8 O 3.6390 6.0980 -4.7310 -0.8340
QMMM: 1 H 4.0990 5.3940 -5.1280 0.4170
QMMM: 1 H 2.7550 5.7240 -4.6570 0.4170
QMMM: 8 O -3.9870 6.0850 -6.6740 -0.8340
QMMM: 1 H -3.9840 6.0350 -5.7080 0.4170
QMMM: 1 H -4.7510 5.5160 -6.9540 0.4170
QMMM: 8 O -8.4380 -3.4640 2.2390 -0.8340
QMMM: 1 H -9.0400 -2.7500 2.0490 0.4170
QMMM: 1 H -8.8030 -4.1730 1.5530 0.4170
QMMM: 8 O -8.6860 -0.6150 -2.8270 -0.8340
QMMM: 1 H -8.6670 -1.2940 -3.5560 0.4170
QMMM: 1 H -7.9440 -0.0470 -3.0200 0.4170
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
QMMM: System specified with odd number of electrons ( 1)
QMMM: but odd spin ( 1). You most likely have the charge of
QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run calculation.
SQM process error. Number of remaining attempts = 0
Printing out the last 150 lines of output...
QMMM: 1 H 3.2560 6.3850 0.1070 0.4170
QMMM: 1 H 3.6160 7.3370 -0.9530 0.4170
QMMM: 8 O 5.3160 -6.0240 5.0330 -0.8340
QMMM: 1 H 5.3530 -5.7350 4.0650 0.4170
QMMM: 1 H 4.5850 -5.4670 5.4600 0.4170
QMMM: 8 O -1.6000 -4.4480 3.5570 -0.8340
QMMM: 1 H -0.9300 -4.7600 4.1850 0.4170
QMMM: 1 H -2.2610 -4.0550 4.1630 0.4170
QMMM: 8 O 5.4650 -2.0450 7.8140 -0.8340
QMMM: 1 H 5.1500 -2.0210 6.9320 0.4170
QMMM: 1 H 4.7060 -2.4370 8.3060 0.4170
QMMM: 8 O -0.9840 -5.9140 -1.1860 -0.8340
QMMM: 1 H -0.6230 -4.9990 -1.1870 0.4170
QMMM: 1 H -1.2740 -6.2590 -0.3390 0.4170
QMMM: 8 O 8.6370 -1.0100 -5.3840 -0.8340
QMMM: 1 H 7.7860 -1.3790 -5.4870 0.4170
QMMM: 1 H 8.5940 -0.0670 -5.3750 0.4170
QMMM: 8 O -3.5610 -4.8560 -2.5450 -0.8340
QMMM: 1 H -2.6900 -5.1640 -2.1630 0.4170
QMMM: 1 H -3.8790 -4.1810 -1.8840 0.4170
QMMM: 8 O 2.0760 -5.3550 3.5660 -0.8340
QMMM: 1 H 2.0000 -4.4780 3.1480 0.4170
QMMM: 1 H 1.8270 -5.1650 4.4430 0.4170
QMMM: 8 O 7.7910 2.2600 -5.2550 -0.8340
QMMM: 1 H 7.3290 3.0950 -5.3870 0.4170
QMMM: 1 H 8.0040 2.3020 -4.3720 0.4170
QMMM: 8 O 5.7420 -8.1750 -0.2260 -0.8340
QMMM: 1 H 6.6990 -8.4460 -0.2710 0.4170
QMMM: 1 H 5.2490 -8.8260 0.3710 0.4170
QMMM: 8 O -2.3060 -1.6620 6.6870 -0.8340
QMMM: 1 H -2.6770 -1.9190 7.5080 0.4170
QMMM: 1 H -3.0090 -1.5240 6.0720 0.4170
QMMM: 8 O 8.3380 0.9700 0.1190 -0.8340
QMMM: 1 H 9.0880 0.5630 0.5320 0.4170
QMMM: 1 H 8.3110 0.5910 -0.7830 0.4170
QMMM: 8 O 0.4070 -3.3510 -1.1120 -0.8340
QMMM: 1 H -0.1900 -2.7850 -0.6140 0.4170
QMMM: 1 H 1.0770 -3.5830 -0.4530 0.4170
QMMM: 8 O 1.3160 -7.7270 -2.0440 -0.8340
QMMM: 1 H 1.3910 -8.6420 -1.8490 0.4170
QMMM: 1 H 0.4230 -7.5210 -1.8190 0.4170
QMMM: 8 O 4.0360 -2.2700 -3.3560 -0.8340
QMMM: 1 H 4.3580 -2.8620 -2.6540 0.4170
QMMM: 1 H 3.8860 -1.4110 -2.8770 0.4170
QMMM: 8 O 7.8170 2.7600 -2.5780 -0.8340
QMMM: 1 H 8.1060 2.6600 -1.6120 0.4170
QMMM: 1 H 7.1600 3.4830 -2.5530 0.4170
QMMM: 8 O 7.9370 -5.3430 1.2030 -0.8340
QMMM: 1 H 7.9180 -6.0780 1.8790 0.4170
QMMM: 1 H 7.7040 -5.8270 0.4150 0.4170
QMMM: 8 O -1.1000 -2.6900 1.2900 -0.8340
QMMM: 1 H -1.2610 -3.2940 2.0780 0.4170
QMMM: 1 H -0.4450 -1.9970 1.5310 0.4170
QMMM: 8 O 8.9060 0.6850 5.0930 -0.8340
QMMM: 1 H 8.5200 1.1950 4.3830 0.4170
QMMM: 1 H 8.2730 -0.0040 5.2720 0.4170
QMMM: 8 O 7.5170 1.8580 3.0100 -0.8340
QMMM: 1 H 7.6400 1.7730 2.0390 0.4170
QMMM: 1 H 7.2890 2.7810 3.1300 0.4170
QMMM: 8 O -0.5050 4.4160 -8.0210 -0.8340
QMMM: 1 H 0.3540 4.2030 -8.4520 0.4170
QMMM: 1 H -0.8350 3.5660 -7.9010 0.4170
QMMM: 8 O 4.6820 1.3340 4.3880 -0.8340
QMMM: 1 H 5.2360 1.9410 3.8760 0.4170
QMMM: 1 H 4.2660 0.6830 3.7630 0.4170
QMMM: 8 O 2.4140 -0.9960 3.9090 -0.8340
QMMM: 1 H 1.5230 -1.0690 4.1840 0.4170
QMMM: 1 H 2.3750 -0.2340 3.2860 0.4170
QMMM: 8 O -2.6660 7.9730 -2.9100 -0.8340
QMMM: 1 H -2.4290 8.3900 -3.8000 0.4170
QMMM: 1 H -3.4670 7.4440 -3.1150 0.4170
QMMM: 8 O 3.9120 1.0400 7.3830 -0.8340
QMMM: 1 H 3.9130 0.9320 6.4230 0.4170
QMMM: 1 H 3.6120 1.9350 7.5180 0.4170
QMMM: 8 O 6.5080 -0.4220 -2.3190 -0.8340
QMMM: 1 H 6.2440 -0.9620 -3.0660 0.4170
QMMM: 1 H 7.3040 0.0210 -2.4840 0.4170
QMMM: 8 O -3.7450 -0.1980 -9.6360 -0.8340
QMMM: 1 H -3.0460 -0.8790 -9.3290 0.4170
QMMM: 1 H -4.5410 -0.7360 -9.8040 0.4170
QMMM: 8 O -3.8600 -6.3310 -6.2960 -0.8340
QMMM: 1 H -3.2680 -6.1630 -7.0510 0.4170
QMMM: 1 H -3.1930 -6.5920 -5.6220 0.4170
QMMM: 8 O -9.5510 -2.6340 -0.8600 -0.8340
QMMM: 1 H -9.7980 -3.5210 -0.9050 0.4170
QMMM: 1 H -9.2040 -2.4370 -1.7440 0.4170
QMMM: 8 O -4.8500 1.6850 1.9940 -0.8340
QMMM: 1 H -4.6880 2.6410 2.0200 0.4170
QMMM: 1 H -4.3860 1.4050 2.7780 0.4170
QMMM: 8 O -7.8210 3.4640 -2.8230 -0.8340
QMMM: 1 H -7.2810 4.0610 -2.2630 0.4170
QMMM: 1 H -8.3600 3.0210 -2.1570 0.4170
QMMM: 8 O -0.9840 5.6900 -0.5150 -0.8340
QMMM: 1 H -0.8420 4.7690 -0.2990 0.4170
QMMM: 1 H -1.4630 5.5540 -1.3480 0.4170
QMMM: 8 O -4.7210 -4.2450 1.4570 -0.8340
QMMM: 1 H -5.4960 -4.6670 0.9670 0.4170
QMMM: 1 H -4.4360 -5.0140 2.0190 0.4170
QMMM: 8 O -9.3250 1.5740 0.9520 -0.8340
QMMM: 1 H -8.4030 1.5460 0.5740 0.4170
QMMM: 1 H -9.7350 2.1500 0.3390 0.4170
QMMM: 8 O -2.1660 4.4080 -2.4730 -0.8340
QMMM: 1 H -2.8950 4.7170 -3.0070 0.4170
QMMM: 1 H -1.8060 3.7140 -3.0740 0.4170
QMMM: 8 O -4.3330 1.8120 9.5420 -0.8340
QMMM: 1 H -4.3530 2.7430 9.4970 0.4170
QMMM: 1 H -4.1110 1.6290 8.6180 0.4170
QMMM: 8 O -1.8440 7.5640 1.5200 -0.8340
QMMM: 1 H -1.6450 8.3450 0.9210 0.4170
QMMM: 1 H -1.6660 6.8200 0.8740 0.4170
QMMM: 8 O -7.4170 6.1230 2.0460 -0.8340
QMMM: 1 H -6.5090 6.5080 2.0590 0.4170
QMMM: 1 H -7.6880 6.3120 2.8870 0.4170
QMMM: 8 O -1.4220 -9.1680 -3.6490 -0.8340
QMMM: 1 H -2.0720 -9.4700 -4.3070 0.4170
QMMM: 1 H -1.4370 -8.1990 -3.6650 0.4170
QMMM: 8 O -2.7130 0.1720 3.8150 -0.8340
QMMM: 1 H -3.3690 -0.5270 4.0770 0.4170
QMMM: 1 H -1.8810 -0.3310 3.8520 0.4170
QMMM: 8 O -1.4390 0.9240 6.8810 -0.8340
QMMM: 1 H -2.0840 1.1880 6.2020 0.4170
QMMM: 1 H -1.6910 0.0080 7.1230 0.4170
QMMM: 8 O -2.1110 6.9970 4.3600 -0.8340
QMMM: 1 H -2.0650 7.1810 3.3580 0.4170
QMMM: 1 H -1.3980 7.5620 4.7340 0.4170
QMMM: 8 O -4.6520 5.4590 -4.0120 -0.8340
QMMM: 1 H -5.0580 6.2110 -3.5350 0.4170
QMMM: 1 H -5.0360 4.6790 -3.5780 0.4170
QMMM: 8 O -8.6880 3.5770 3.8290 -0.8340
QMMM: 1 H -8.4060 3.3500 2.9630 0.4170
QMMM: 1 H -9.0950 4.4430 3.6340 0.4170
QMMM: 8 O 3.6390 6.0980 -4.7310 -0.8340
QMMM: 1 H 4.0990 5.3940 -5.1280 0.4170
QMMM: 1 H 2.7550 5.7240 -4.6570 0.4170
QMMM: 8 O -3.9870 6.0850 -6.6740 -0.8340
QMMM: 1 H -3.9840 6.0350 -5.7080 0.4170
QMMM: 1 H -4.7510 5.5160 -6.9540 0.4170
QMMM: 8 O -8.4380 -3.4640 2.2390 -0.8340
QMMM: 1 H -9.0400 -2.7500 2.0490 0.4170
QMMM: 1 H -8.8030 -4.1730 1.5530 0.4170
QMMM: 8 O -8.6860 -0.6150 -2.8270 -0.8340
QMMM: 1 H -8.6670 -1.2940 -3.5560 0.4170
QMMM: 1 H -7.9440 -0.0470 -3.0200 0.4170
--------------------------------------------------------------------------------
QM CALCULATION INFO
--------------------------------------------------------------------------------
QMMM: System specified with odd number of electrons ( 1)
QMMM: but odd spin ( 1). You most likely have the charge of
QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run calculation.
Traceback (most recent call last):
File "sample.py", line 115, in <module>
print("Total QM/MM energy = %s" % system.energy(e_qmmm))
UserWarning: Exception 'SireError::process_error' thrown by the thread 'master'.
Could not find the total energy in the SQM output!
Thrown from FILE: /home/riccardo/Sire-feature-charmmff/corelib/src/libs/Squire/sqm.cpp, LINE: 702, FUNCTION: double Squire::SQM::extractEnergy(QFile&) const
__Backtrace__
( 0) /home/riccardo/sire.app/bin/../lib/./libSireError.so.2017 ([0x7f66f154d4b1] ++0x41)
-- SireError::getBackTrace()
( 1) /home/riccardo/sire.app/bin/../lib/./libSireError.so.2017 ([0x7f66f154a05b] ++0xab)
-- SireError::exception::exception(QString, QString)
/home/riccardo/sire.app/bin/../lib/libSquire.so.2017(+0x5f992) [0x7f66ddd01992]
( 3) /home/riccardo/sire.app/bin/../lib/libSquire.so.2017 ([0x7f66ddd6ae54] ++0x5e4)
-- Squire::SQM::extractEnergy(QFile&) const
( 4) /home/riccardo/sire.app/bin/../lib/libSquire.so.2017 ([0x7f66ddd6c748] ++0x7d8)
-- Squire::SQM::calculateEnergy(QString const&, int) const
( 5) /home/riccardo/sire.app/bin/../lib/libSquire.so.2017 ([0x7f66ddd6d4dc] ++0x156c)
-- Squire::SQM::calculateEnergy(QString const&, int) const
( 6) /home/riccardo/sire.app/bin/../lib/libSquire.so.2017 ([0x7f66ddd6d4dc] ++0x156c)
-- Squire::SQM::calculateEnergy(QString const&, int) const
( 7) /home/riccardo/sire.app/bin/../lib/libSquire.so.2017 ([0x7f66ddd6d4dc] ++0x156c)
-- Squire::SQM::calculateEnergy(QString const&, int) const
( 8) /home/riccardo/sire.app/bin/../lib/libSquire.so.2017 ([0x7f66ddd6d4dc] ++0x156c)
-- Squire::SQM::calculateEnergy(QString const&, int) const
( 9) /home/riccardo/sire.app/bin/../lib/libSquire.so.2017 ([0x7f66ddd6d4dc] ++0x156c)
-- Squire::SQM::calculateEnergy(QString const&, int) const
( 10) /home/riccardo/sire.app/bin/../lib/libSquire.so.2017 ([0x7f66ddd6dc29] ++0x89)
-- Squire::SQM::calculateEnergy(SireFF::detail::FFMolecules3D<Squire::QMPotential> const&, Squire::LatticeCharges const&, int) const
( 11) /home/riccardo/sire.app/bin/../lib/libSquire.so.2017 ([0x7f66ddd22b65] ++0xa5)
-- Squire::QMMMElecEmbedPotential::calculateEnergy(SireFF::detail::FFMolecules3D<Squire::QMPotential> const&, SireFF::detail::FFMolecules3D<SireMM::InterCoulombPotential> const&, SireFF::ComponentEnergy<Squire::QMComponent>&, double) const
( 12) /home/riccardo/sire.app/bin/../lib/libSquire.so.2017 ([0x7f66ddd329e2] ++0x52)
-- Squire::QMMMFF::recalculateEnergy()
( 13) /home/riccardo/sire.app/bin/../lib/./libSireFF.so.2017 ([0x7f66ec08436c] ++0xac)
-- SireFF::FF::energy(SireCAS::Symbol const&)
/home/riccardo/sire.app/bin/../lib/./libSireFF.so.2017(+0xb17f8) [0x7f66ec0bc7f8]
/home/riccardo/sire.app/bin/../lib/./libtbb.so.2(+0x2705b) [0x7f66ef9e705b]
/home/riccardo/sire.app/bin/../lib/./libtbb.so.2(+0x20122) [0x7f66ef9e0122]
/home/riccardo/sire.app/bin/../lib/./libtbb.so.2(+0x1eba4) [0x7f66ef9deba4]
/home/riccardo/sire.app/bin/../lib/./libtbb.so.2(+0x1ada6) [0x7f66ef9dada6]
/home/riccardo/sire.app/bin/../lib/./libtbb.so.2(+0x1aff9) [0x7f66ef9daff9]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x76ba) [0x7f66f3b096ba]
( 21) /lib/x86_64-linux-gnu/libc.so.6 ([0x7f66f2f2741d] ++0x6d)
-- clone
__EndTrace__
Exception 'SireError::process_error' thrown by the thread 'master'.
Could not find the total energy in the SQM output!
Thrown from FILE: /home/riccardo/Sire-feature-charmmff/corelib/src/libs/Squire/sqm.cpp, LINE: 702, FUNCTION: double Squire::SQM::extractEnergy(QFile&) const
Christopher Woods
Mar 7, 2018, 4:10:47 AM3/7/18
to sire-...@googlegroups.com
Hi Riccardo,
It looks like you are seeing a similar problem, although I am not sure why as the code given in the script was merged into post 2014.X versions of Sire and should already be in the 2017.3 version. Could you email me your input files so that I can build a unit test and debug the problem? I can then create an update for you that should fix things.
Best wishes,
Christopher
p.s. I notice that your directory is called Sire-feature-charmmff. Sire doesn't yet fully support the charmm forcefield (it is currently work in progress). Are you using charmm? For an ion in water things should be fine, but I would be concerned if you started looking at molecules in water.
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Riccardo Ocello
Mar 7, 2018, 6:20:14 AM3/7/18
to Sire Users
Dear Christopher,
first of all thanks for your kind reply (here and in the other post..I'll reply there in few minutes!).
In principle I tried to use that version hoping that it works with Charmm, but after some trials I realized that it doesn't. Anyway, I build this small test case using tleap (and Amberff14SB), thus the right way (I guess).
To fix this error, I replaced the file suggested to Gaetano in my Sire bin ( /home/riccardo/sire.app/lib/python3.5/site-packages/Sire/Tools ), but i doesn't work again.
Here attached you find my input files.
Thanks for your availability!
Riccardo
...
Christopher Woods
Mar 9, 2018, 12:31:35 PM3/9/18
to sire-...@googlegroups.com
Hi Riccardo,
Could you send me the command you are using to run quantomm? I am trying to run it but am getting errors because the crd/top file you have sent don't appear to have any periodic box information? The program needs the top/crd file to include the periodic box for quantomm to work.
Best wishes,
Christopher
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Riccardo Ocello
Mar 12, 2018, 6:39:58 AM3/12/18
to Sire Users
Dear Christopher,
sorry for the late reply. This is the command:
$SIRE/python ../sample.py K+ AM1
where sample.py is the "config" file found in quantomm Tutorial. I'm using Amber16 as MD engine for SQM calculation and system setup (top/crd).
Cheers,
Riccardo
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