Constraint SireSystem::SpaceWrapper() is not satisfied despite having just been applied!!!

[jm1...@my.bristol.ac.uk]

Hi,

When trying to use quantomm to perturb a TIP3P water molecule solvated by TIP3P using dftb methods I've encountered this error:

Traceback (most recent call last):
File "/users/jm15465/sire.app/pkgs/sire-2017.3.0/share/Sire/scripts/quantomm.py", line 237, in <module>
QuantumToMM.run(params)
File "/users/jm15465/sire.app/lib/python3.5/site-packages/Sire/Tools/__init__.py", line 172, in inner
retval = func()
File "/users/jm15465/sire.app/lib/python3.5/site-packages/Sire/Tools/QuantumToMM.py", line 1052, in run
(qm_system,qm_moves) = loadQMMM()
File "/users/jm15465/sire.app/lib/python3.5/site-packages/Sire/Tools/QuantumToMM.py", line 966, in loadQMMM
system = loadQMMMSystem()
File "/users/jm15465/sire.app/lib/python3.5/site-packages/Sire/Tools/QuantumToMM.py", line 443, in loadQMMMSystem
loadsys = createSystem(topfile.val, crdfile.val, sys_scheme)
File "/users/jm15465/sire.app/lib/python3.5/site-packages/Sire/Tools/AmberLoader.py", line 401, in createSystem
return createSystemFrom(system[MGIdx(0)], system.property("space"), top_file, naming_scheme)
File "/users/jm15465/sire.app/lib/python3.5/site-packages/Sire/Tools/AmberLoader.py", line 381, in createSystemFrom
system.add( SpaceWrapper( Vector(0), all_group ) )
UserWarning: Exception 'SireError::program_bug' thrown by the thread 'master:main'.
Constraint SireSystem::SpaceWrapper() is not satisfied despite having just been applied!!!
Thrown from FILE: /home/chris/Sire/corelib/src/libs/SireSystem/constraint.cpp, LINE: 167, FUNCTION: bool SireSystem::Constraint::apply(SireSystem::Delta&)
__Backtrace__
( 0) /users/jm15465/sire.app/bin/../lib/libSireError.so.2017 ([0x2acdfbbbbcce] ++0x2e)
-- SireError::getBackTrace()

( 1) /users/jm15465/sire.app/bin/../lib/libSireError.so.2017 ([0x2acdfbbb8a76] ++0x86)
-- SireError::exception::exception(QString, QString)

/users/jm15465/sire.app/bin/../lib/libSireSystem.so.2017(+0x8d232) [0x2acdf8ded232]
( 3) /users/jm15465/sire.app/bin/../lib/libSireSystem.so.2017 ([0x2acdf8de79bb] ++0x27b)
-- SireSystem::Constraint::apply(SireSystem::Delta&)

( 4) /users/jm15465/sire.app/bin/../lib/libSireSystem.so.2017 ([0x2acdf8df2a74] ++0x684)
-- SireSystem::Constraints::apply(SireSystem::Delta&)

( 5) /users/jm15465/sire.app/bin/../lib/libSireSystem.so.2017 ([0x2acdf8dfbae1] ++0x31)
-- SireSystem::Delta::apply()

( 6) /users/jm15465/sire.app/bin/../lib/libSireSystem.so.2017 ([0x2acdf8e836c4] ++0x34)
-- SireSystem::System::applyAllConstraints()

( 7) /users/jm15465/sire.app/bin/../lib/libSireSystem.so.2017 ([0x2acdf8e83aab] ++0x5b)
-- SireSystem::System::add(SireSystem::Constraints const&)

( 8) /users/jm15465/sire.app/bin/../lib/libSireSystem.so.2017 ([0x2acdf8e83b2f] ++0x1f)
-- SireSystem::System::add(SireSystem::Constraint const&)

/users/jm15465/sire.app/lib/python3.5/site-packages/Sire/System/_System.so(+0xe2840) [0x2ace06e82840]
( 10) /users/jm15465/sire.app/bin/../lib/libboost_python.so ([0x2acdf48e04d7] ++0x2d7)
-- boost::python::objects::function::call(_object*, _object*) const

/users/jm15465/sire.app/bin/../lib/libboost_python.so(+0x30698) [0x2acdf48e0698]
( 12) /users/jm15465/sire.app/bin/../lib/libboost_python.so ([0x2acdf48d51db] ++0x4b)
-- boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const

/users/jm15465/sire.app/lib/python3.5/site-packages/Sire/Error/_Error.so(+0x250d) [0x2acdff6e250d]
( 14) /users/jm15465/sire.app/bin/../lib/libboost_python.so ([0x2acdf48d51ba] ++0x2a)
-- boost::python::detail::exception_handler::operator()(boost::function0<void> const&) const

/users/jm15465/sire.app/lib/python3.5/site-packages/Sire/Error/_Error.so(+0x24cb) [0x2acdff6e24cb]
( 16) /users/jm15465/sire.app/bin/../lib/libboost_python.so ([0x2acdf48d4faf] ++0x2f)
-- boost::python::handle_exception_impl(boost::function0<void>)

/users/jm15465/sire.app/bin/../lib/libboost_python.so(+0x2ddf9) [0x2acdf48dddf9]
( 18) /users/jm15465/sire.app/bin/../lib/libpython3.5m.so.1.0 ([0x2acdf4427236] ++0x56)
-- PyObject_Call

( 19) /users/jm15465/sire.app/bin/../lib/libpython3.5m.so.1.0 ([0x2acdf4501314] ++0x66f4)
-- PyEval_EvalFrameEx

/users/jm15465/sire.app/bin/../lib/libpython3.5m.so.1.0(+0x144b49) [0x2acdf4504b49]
( 21) /users/jm15465/sire.app/bin/../lib/libpython3.5m.so.1.0 ([0x2acdf4503df5] ++0x91d5)
-- PyEval_EvalFrameEx

/users/jm15465/sire.app/bin/../lib/libpython3.5m.so.1.0(+0x144b49) [0x2acdf4504b49]
( 23) /users/jm15465/sire.app/bin/../lib/libpython3.5m.so.1.0 ([0x2acdf4503df5] ++0x91d5)
-- PyEval_EvalFrameEx

( 24) /users/jm15465/sire.app/bin/../lib/libpython3.5m.so.1.0 ([0x2acdf4504166] ++0x9546)
-- PyEval_EvalFrameEx

( 25) /users/jm15465/sire.app/bin/../lib/libpython3.5m.so.1.0 ([0x2acdf4504166] ++0x9546)
-- PyEval_EvalFrameEx

( 26) /users/jm15465/sire.app/bin/../lib/libpython3.5m.so.1.0 ([0x2acdf4504166] ++0x9546)
-- PyEval_EvalFrameEx

/users/jm15465/sire.app/bin/../lib/libpython3.5m.so.1.0(+0x144b49) [0x2acdf4504b49]
( 28) /users/jm15465/sire.app/bin/../lib/libpython3.5m.so.1.0 ([0x2acdf4503df5] ++0x91d5)
-- PyEval_EvalFrameEx

/users/jm15465/sire.app/bin/../lib/libpython3.5m.so.1.0(+0x144b49) [0x2acdf4504b49]
( 30) /users/jm15465/sire.app/bin/../lib/libpython3.5m.so.1.0 ([0x2acdf4504cd8] ++0x48)
-- PyEval_EvalCodeEx

( 31) /users/jm15465/sire.app/bin/../lib/libpython3.5m.so.1.0 ([0x2acdf4504d1b] ++0x3b)
-- PyEval_EvalCode

( 32) /users/jm15465/sire.app/bin/../lib/libpython3.5m.so.1.0 ([0x2acdf452a020] ++0x130)
-- PyRun_FileExFlags

( 33) /users/jm15465/sire.app/bin/../lib/libpython3.5m.so.1.0 ([0x2acdf452b623] ++0x173)
-- PyRun_SimpleFileExFlags

( 34) /users/jm15465/sire.app/bin/../lib/libpython3.5m.so.1.0 ([0x2acdf45468c7] ++0xca7)
-- Py_Main

/users/jm15465/sire.app/bin/quantomm() [0x402d6e]
( 36) /lib64/libc.so.6 ([0x361481ed1d] ++0xfd)
-- __libc_start_main

/users/jm15465/sire.app/bin/quantomm() [0x40358d]
__EndTrace__
Exception 'SireError::program_bug' thrown by the thread 'master:main'.
Constraint SireSystem::SpaceWrapper() is not satisfied despite having just been applied!!!
Thrown from FILE: /home/chris/Sire/corelib/src/libs/SireSystem/constraint.cpp, LINE: 167, FUNCTION: bool SireSystem::Constraint::apply(SireSystem::Delta&)

With the stdout being:


Loading configuration information from file config

Running a quantomm calculation using files ../purewater_tip3p.top and ../purewater_min.rst.
The MM to QM/MM correction free energy of the molecule containing residue T3P will be calculated.

Using parameters:
===============
LJ cutoff == 7.5 angstrom
coulomb cutoff == 7.5 angstrom
crdfile == ../purewater_min.rst
intermolecular only == True
ligand name == T3P
qm method == dftb
qm program == sqm
topfile == ../purewater_tip3p.top
===============
Loading the system...
Loading from Amber files ../purewater_tip3p.top / ../purewater_min.rst...
Loading the molecules from the files "../purewater_min.rst" and "../purewater_tip3p.top"...
Number of molecules == 210
System space == PeriodicBox( ( 22.771, 22.8538, 22.6001 ) )
Assigning molecules to molecule groups...
Number of solute molecules == 1
Number of protein molecules == 0
Number of ions == 0
Number of water molecules == 209
Number of solvent molecules == 209
(solvent group is waters + ions + unidentified single-residue molecules)
Starting /users/jm15465/sire.app/bin/quantomm: number of threads equals 24


Any suggestions on what's going wrong?

[Christopher Woods]

  Hi,

Could you email me the purewater_tip3p.top and purewater_min.rst files as these are triggering a bug in quantomm related to periodic boundary conditions. Sire (on which quantomm is based) has lots of internal checks and tests that are run during a simulation to catch bugs, and your error is because one of these tests has failed. 

You can see this as a "program_bug" exception has been raised, with the test that failed being in Sire/corelib/src/libs/SireSystem/constraint.cpp, LINE: 167

(this file - <https://github.com/michellab/Sire/blob/devel/corelib/src/libs/SireSystem/constraint.cpp>)

This tested whether or not a constraint was satisfied after it was applied (as, logically, after application, it must be satisfied). In your case, the SpaceWrapper constraint, which wraps all molecules back into the central periodic box, is not satisfied despite having been just applied. I've not seen this before with other systems, so would like a copy of your input files so that I can look deeper into why SpaceWrapper is not behaving itself.

  Best wishes,

  Christopher

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---------------------------------------------------------
Christopher Woods
+44 (0) 7786 264562
http://chryswoods.com

[jm1...@my.bristol.ac.uk]

Hi Christopher,

I've attached the relevent files, including the tleap file used to generate the top & crd files, the files themselves and the sander input file used to minimise.

At the moment I've resorted to simply running Quantomm using the crd file, which appears to work fine.

Thanks,
James