Fix AmberPrmtopFile for building with IFBOX != 1 or 2. Also Add tests for a

truncated octahedron inpcrd and prmtop file.

wrappers/python/simtk/openmm/app/internal/amber_file_parser.py

@@ -709,9 +709,6 @@ def readAmberSystem(prmtop_filename=None, prmtop_loader=None, shake=None, gbmode
     if prmtop.getIfPert()>0:
         raise Exception("perturbation not currently supported")
 
-    if prmtop.getIfBox()>1:
-        raise Exception("only standard periodic boxes are currently supported")
-
     if prmtop.has_scee_scnb and (scee is not None or scnb is not None):
         warnings.warn("1-4 scaling parameters in topology file are being ignored. "
             "This is not recommended unless you know what you are doing.")

wrappers/python/tests/TestAmberInpcrdFile.py

@@ -60,5 +60,29 @@ class TestAmberInpcrdFile(unittest.TestCase):
         self.assertTrue(inpcrd.boxVectors is None)
         self.assertTrue(inpcrd.velocities is None)
 
+    def test_CrdBoxTruncoct(self):
+        # Check that the box vectors come out correct.
+        inpcrd = AmberInpcrdFile('systems/tz2.truncoct.rst7')
+        ac = Vec3(42.4388485, 0.0, 0.0) * angstroms
+        bc = Vec3(-14.146281691908937, 40.011730483685835, 0.0) * angstroms
+        cc = Vec3(-14.146281691908937, -20.0058628205162, 34.651176446201672) * angstroms
+        a, b, c = inpcrd.getBoxVectors()
+        diffa = ac - a
+        diffb = bc - b
+        diffc = cc - c
+        self.assertAlmostEqual(norm(diffa)/angstroms, 0)
+        self.assertAlmostEqual(norm(diffb)/angstroms, 0)
+        self.assertAlmostEqual(norm(diffc)/angstroms, 0)
+        # Make sure angles and lengths come out about right
+        la = norm(a).in_units_of(angstroms)
+        lb = norm(b).in_units_of(angstroms)
+        lc = norm(c).in_units_of(angstroms)
+        self.assertAlmostEqual(la/angstroms, 42.4388485, 6)
+        self.assertAlmostEqual(lb/angstroms, 42.4388485, 6)
+        self.assertAlmostEqual(lc/angstroms, 42.4388485, 6)
+        self.assertAlmostEqual(dot(a,b)/la/lb, cos(109.4712190*degrees), 6)
+        self.assertAlmostEqual(dot(a,c)/la/lc, cos(109.4712190*degrees), 6)
+        self.assertAlmostEqual(dot(b,c)/lc/lb, cos(109.4712190*degrees), 6)
+
 if __name__ == '__main__':
     unittest.main()

wrappers/python/tests/TestAmberPrmtopFile.py

@@ -9,6 +9,7 @@ prmtop1 = AmberPrmtopFile('systems/alanine-dipeptide-explicit.prmtop')
 prmtop2 = AmberPrmtopFile('systems/alanine-dipeptide-implicit.prmtop')
 prmtop3 = AmberPrmtopFile('systems/ff14ipq.parm7')
 prmtop4 = AmberPrmtopFile('systems/Mg_water.prmtop')
+prmtop5 = AmberPrmtopFile('systems/tz2.truncoct.parm7')
 inpcrd3 = AmberInpcrdFile('systems/ff14ipq.rst7')
 inpcrd4 = AmberInpcrdFile('systems/Mg_water.inpcrd')
 
@@ -230,6 +231,31 @@ class TestAmberPrmtopFile(unittest.TestCase):
         # Amber using this force field.
         self.assertAlmostEqual(-7307.2735621/ene, 1, places=3)
 
+    def test_triclinicParm(self):
+        """ Check that triclinic unit cells work correctly """
+        system = prmtop5.createSystem(nonbondedMethod=PME)
+        refa = Vec3(4.48903851, 0.0, 0.0) * nanometer
+        refb = Vec3(-1.4963460492639706, 4.232306137924705, 0.0) * nanometer
+        refc = Vec3(-1.4963460492639706, -2.116152812842565, 3.6652847799064165) * nanometer
+        a, b, c = system.getDefaultPeriodicBoxVectors()
+        la = norm(a)
+        lb = norm(b)
+        lc = norm(c)
+        diffa = a - refa
+        diffb = b - refb
+        diffc = c - refc
+        self.assertAlmostEqual(norm(diffa)/nanometers, 0)
+        self.assertAlmostEqual(norm(diffb)/nanometers, 0)
+        self.assertAlmostEqual(norm(diffc)/nanometers, 0)
+        self.assertAlmostEqual(dot(a, b)/la/lb, cos(109.4712190*degrees))
+        self.assertAlmostEqual(dot(a, c)/la/lc, cos(109.4712190*degrees))
+        self.assertAlmostEqual(dot(c, b)/lc/lb, cos(109.4712190*degrees))
+        self.assertAlmostEqual(la/nanometers, 4.48903851)
+        self.assertAlmostEqual(lb/nanometers, 4.48903851)
+        self.assertAlmostEqual(lc/nanometers, 4.48903851)
+        # Now make sure that the context builds correctly; then we can bail
+        self.assertTrue(Context(system, VerletIntegrator(1*femtoseconds)))
+
     def test_ImplicitSolventForces(self):
         """Compute forces for different implicit solvent types, and compare them to ones generated with a previous version of OpenMM to ensure they haven't changed."""