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[BUG] ParmEd box vectors are occasionally incompatible with OpenMM #134

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lohedges opened this issue Jul 11, 2023 · 0 comments · Fixed by #135
Closed

[BUG] ParmEd box vectors are occasionally incompatible with OpenMM #134

lohedges opened this issue Jul 11, 2023 · 0 comments · Fixed by #135
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bug Something isn't working exscientia Related to work with Exscientia

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@lohedges
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Occasionally triclinic box vectors generated by parmed (having read box dimensions and angles from AMBER rst7 format) are incompatible with openmm, which raises the following exception:

Traceback (most recent call last):
  File "test1/run.py", line 146, in <module>
  File "test1/run.py", line 56, in test_openmm
  File ".../openmm/openmm.py", line 2292, in setPeriodicBoxVectors
    return _openmm.Context_setPeriodicBoxVectors(self, a, b, c)
openmm.OpenMMException: Periodic box vectors must be in reduced form.

This can be avoided by passing the parmed box vectors through the internal openmm.app.internal.unitcell.reducePeriodicBoxVectors function before passing them through to the context.

@lohedges lohedges added bug Something isn't working exscientia Related to work with Exscientia labels Jul 11, 2023
lohedges added a commit that referenced this issue Jul 11, 2023
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Labels
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