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Commit 4f11c10f authored by Rafal P. Wiewiora's avatar Rafal P. Wiewiora
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move PDB to systems

parent 311cc01e
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wrappers/python/tests/TestForceField.py
View file @ 4f11c10f
...@@ -774,69 +774,6 @@ class TestForceField(unittest.TestCase): ...@@ -774,69 +774,6 @@ class TestForceField(unittest.TestCase):
and the torsion.ordering parameter. and the torsion.ordering parameter.
""" """
pdb = """
ATOM 1 N LEU A 1 25.160 14.160 19.440 1.00 0.00 N
ATOM 2 H1 LEU A 1 24.224 13.904 20.146 1.00 0.00 H
ATOM 3 H2 LEU A 1 25.993 13.474 19.964 1.00 0.00 H
ATOM 4 H3 LEU A 1 25.448 15.264 19.811 1.00 0.00 H
ATOM 5 CA LEU A 1 25.090 13.920 17.980 1.00 0.00 C
ATOM 6 HA LEU A 1 24.679 12.800 17.995 1.00 0.00 H
ATOM 7 CB LEU A 1 24.420 14.970 17.100 1.00 0.00 C
ATOM 8 HB3 LEU A 1 24.592 14.703 15.949 1.00 0.00 H
ATOM 9 HB2 LEU A 1 24.907 16.046 17.290 1.00 0.00 H
ATOM 10 CG LEU A 1 22.930 15.010 17.400 1.00 0.00 C
ATOM 11 HG LEU A 1 22.677 15.678 18.357 1.00 0.00 H
ATOM 12 CD1 LEU A 1 22.410 15.830 16.210 1.00 0.00 C
ATOM 13 HD11 LEU A 1 22.229 15.260 15.170 1.00 0.00 H
ATOM 14 HD12 LEU A 1 21.323 16.283 16.456 1.00 0.00 H
ATOM 15 HD13 LEU A 1 22.952 16.853 15.894 1.00 0.00 H
ATOM 16 CD2 LEU A 1 22.100 13.730 17.590 1.00 0.00 C
ATOM 17 HD21 LEU A 1 22.228 12.870 16.765 1.00 0.00 H
ATOM 18 HD22 LEU A 1 22.102 13.167 18.648 1.00 0.00 H
ATOM 19 HD23 LEU A 1 20.924 13.966 17.534 1.00 0.00 H
ATOM 20 C LEU A 1 26.520 13.970 17.430 1.00 0.00 C
ATOM 21 O LEU A 1 27.360 14.710 17.880 1.00 0.00 O
ATOM 22 N SER A 2 26.720 13.080 16.460 1.00 0.00 N
ATOM 23 H SER A 2 26.006 12.134 16.365 1.00 0.00 H
ATOM 24 CA SER A 2 27.950 12.790 15.610 1.00 0.00 C
ATOM 25 HA SER A 2 28.762 12.484 16.429 1.00 0.00 H
ATOM 26 CB SER A 2 27.740 11.640 14.610 1.00 0.00 C
ATOM 27 HB3 SER A 2 28.674 11.459 13.887 1.00 0.00 H
ATOM 28 HB2 SER A 2 26.789 11.677 13.883 1.00 0.00 H
ATOM 29 OG SER A 2 27.520 10.520 15.410 1.00 0.00 O
ATOM 30 HG SER A 2 27.939 9.540 14.882 1.00 0.00 H
ATOM 31 C SER A 2 28.360 14.010 14.820 1.00 0.00 C
ATOM 32 O SER A 2 27.440 14.680 14.350 1.00 0.00 O
ATOM 33 N ASP A 3 29.650 14.360 14.620 1.00 0.00 N
ATOM 34 H ASP A 3 30.534 13.595 14.830 1.00 0.00 H
ATOM 35 CA ASP A 3 29.940 15.810 14.230 1.00 0.00 C
ATOM 36 HA ASP A 3 29.441 16.464 15.093 1.00 0.00 H
ATOM 37 CB ASP A 3 31.420 16.030 14.240 1.00 0.00 C
ATOM 38 HB3 ASP A 3 32.161 15.358 13.586 1.00 0.00 H
ATOM 39 HB2 ASP A 3 31.910 15.981 15.330 1.00 0.00 H
ATOM 40 CG ASP A 3 31.690 17.460 13.840 1.00 0.00 C
ATOM 41 OD1 ASP A 3 31.390 18.400 14.660 1.00 0.00 O
ATOM 42 OD2 ASP A 3 32.230 17.650 12.700 1.00 0.00 O
ATOM 43 C ASP A 3 29.350 16.300 12.880 1.00 0.00 C
ATOM 44 O ASP A 3 28.860 17.390 12.790 1.00 0.00 O
ATOM 45 N GLU A 4 29.370 15.470 11.800 1.00 0.00 N
ATOM 46 H GLU A 4 29.943 14.435 11.896 1.00 0.00 H
ATOM 47 CA GLU A 4 28.630 15.770 10.590 1.00 0.00 C
ATOM 48 HA GLU A 4 28.813 16.889 10.221 1.00 0.00 H
ATOM 49 CB GLU A 4 29.000 14.740 9.500 1.00 0.00 C
ATOM 50 HB3 GLU A 4 28.209 14.877 8.613 1.00 0.00 H
ATOM 51 HB2 GLU A 4 28.927 13.570 9.734 1.00 0.00 H
ATOM 52 CG GLU A 4 30.400 15.140 9.010 1.00 0.00 C
ATOM 53 HG3 GLU A 4 31.338 14.917 9.713 1.00 0.00 H
ATOM 54 HG2 GLU A 4 30.559 16.245 8.583 1.00 0.00 H
ATOM 55 CD GLU A 4 30.820 14.370 7.750 1.00 0.00 C
ATOM 56 OE1 GLU A 4 31.770 13.490 7.830 1.00 0.00 O
ATOM 57 OE2 GLU A 4 30.220 14.580 6.660 1.00 0.00 O
ATOM 58 C GLU A 4 27.080 15.870 10.880 1.00 0.00 C
ATOM 59 O GLU A 4 26.440 16.810 10.390 1.00 0.00 O
ATOM 60 OXT GLU A 4 26.692 14.850 11.569 1.00 0.00 O
"""
xml = """ xml = """
<ForceField> <ForceField>
<PeriodicTorsionForce ordering="amber"> <PeriodicTorsionForce ordering="amber">
...@@ -844,14 +781,14 @@ ATOM 60 OXT GLU A 4 26.692 14.850 11.569 1.00 0.00 O ...@@ -844,14 +781,14 @@ ATOM 60 OXT GLU A 4 26.692 14.850 11.569 1.00 0.00 O
</PeriodicTorsionForce> </PeriodicTorsionForce>
</ForceField> </ForceField>
""" """
pdb_ = PDBFile(StringIO(pdb)) pdb = PDBFile('systems/impropers_ordering_tetrapeptide.pdb')
# ff1 uses default ordering of impropers, ff2 uses "amber" for the one # ff1 uses default ordering of impropers, ff2 uses "amber" for the one
# problematic improper # problematic improper
ff1 = ForceField('amber99sbildn.xml') ff1 = ForceField('amber99sbildn.xml')
ff2 = ForceField(StringIO(xml), 'amber99sbildn.xml') ff2 = ForceField(StringIO(xml), 'amber99sbildn.xml')
system1 = ff1.createSystem(pdb_.topology) system1 = ff1.createSystem(pdb.topology)
system2 = ff2.createSystem(pdb_.topology) system2 = ff2.createSystem(pdb.topology)
imp1 = system1.getForce(2).getTorsionParameters(158) imp1 = system1.getForce(2).getTorsionParameters(158)
imp2 = system2.getForce(0).getTorsionParameters(158) imp2 = system2.getForce(0).getTorsionParameters(158)
......
wrappers/python/tests/systems/impropers_ordering_tetrapeptide.pdb 0 → 100644
View file @ 4f11c10f
ATOM 1 N LEU A 1 25.160 14.160 19.440 1.00 0.00 N
ATOM 2 H1 LEU A 1 24.224 13.904 20.146 1.00 0.00 H
ATOM 3 H2 LEU A 1 25.993 13.474 19.964 1.00 0.00 H
ATOM 4 H3 LEU A 1 25.448 15.264 19.811 1.00 0.00 H
ATOM 5 CA LEU A 1 25.090 13.920 17.980 1.00 0.00 C
ATOM 6 HA LEU A 1 24.679 12.800 17.995 1.00 0.00 H
ATOM 7 CB LEU A 1 24.420 14.970 17.100 1.00 0.00 C
ATOM 8 HB3 LEU A 1 24.592 14.703 15.949 1.00 0.00 H
ATOM 9 HB2 LEU A 1 24.907 16.046 17.290 1.00 0.00 H
ATOM 10 CG LEU A 1 22.930 15.010 17.400 1.00 0.00 C
ATOM 11 HG LEU A 1 22.677 15.678 18.357 1.00 0.00 H
ATOM 12 CD1 LEU A 1 22.410 15.830 16.210 1.00 0.00 C
ATOM 13 HD11 LEU A 1 22.229 15.260 15.170 1.00 0.00 H
ATOM 14 HD12 LEU A 1 21.323 16.283 16.456 1.00 0.00 H
ATOM 15 HD13 LEU A 1 22.952 16.853 15.894 1.00 0.00 H
ATOM 16 CD2 LEU A 1 22.100 13.730 17.590 1.00 0.00 C
ATOM 17 HD21 LEU A 1 22.228 12.870 16.765 1.00 0.00 H
ATOM 18 HD22 LEU A 1 22.102 13.167 18.648 1.00 0.00 H
ATOM 19 HD23 LEU A 1 20.924 13.966 17.534 1.00 0.00 H
ATOM 20 C LEU A 1 26.520 13.970 17.430 1.00 0.00 C
ATOM 21 O LEU A 1 27.360 14.710 17.880 1.00 0.00 O
ATOM 22 N SER A 2 26.720 13.080 16.460 1.00 0.00 N
ATOM 23 H SER A 2 26.006 12.134 16.365 1.00 0.00 H
ATOM 24 CA SER A 2 27.950 12.790 15.610 1.00 0.00 C
ATOM 25 HA SER A 2 28.762 12.484 16.429 1.00 0.00 H
ATOM 26 CB SER A 2 27.740 11.640 14.610 1.00 0.00 C
ATOM 27 HB3 SER A 2 28.674 11.459 13.887 1.00 0.00 H
ATOM 28 HB2 SER A 2 26.789 11.677 13.883 1.00 0.00 H
ATOM 29 OG SER A 2 27.520 10.520 15.410 1.00 0.00 O
ATOM 30 HG SER A 2 27.939 9.540 14.882 1.00 0.00 H
ATOM 31 C SER A 2 28.360 14.010 14.820 1.00 0.00 C
ATOM 32 O SER A 2 27.440 14.680 14.350 1.00 0.00 O
ATOM 33 N ASP A 3 29.650 14.360 14.620 1.00 0.00 N
ATOM 34 H ASP A 3 30.534 13.595 14.830 1.00 0.00 H
ATOM 35 CA ASP A 3 29.940 15.810 14.230 1.00 0.00 C
ATOM 36 HA ASP A 3 29.441 16.464 15.093 1.00 0.00 H
ATOM 37 CB ASP A 3 31.420 16.030 14.240 1.00 0.00 C
ATOM 38 HB3 ASP A 3 32.161 15.358 13.586 1.00 0.00 H
ATOM 39 HB2 ASP A 3 31.910 15.981 15.330 1.00 0.00 H
ATOM 40 CG ASP A 3 31.690 17.460 13.840 1.00 0.00 C
ATOM 41 OD1 ASP A 3 31.390 18.400 14.660 1.00 0.00 O
ATOM 42 OD2 ASP A 3 32.230 17.650 12.700 1.00 0.00 O
ATOM 43 C ASP A 3 29.350 16.300 12.880 1.00 0.00 C
ATOM 44 O ASP A 3 28.860 17.390 12.790 1.00 0.00 O
ATOM 45 N GLU A 4 29.370 15.470 11.800 1.00 0.00 N
ATOM 46 H GLU A 4 29.943 14.435 11.896 1.00 0.00 H
ATOM 47 CA GLU A 4 28.630 15.770 10.590 1.00 0.00 C
ATOM 48 HA GLU A 4 28.813 16.889 10.221 1.00 0.00 H
ATOM 49 CB GLU A 4 29.000 14.740 9.500 1.00 0.00 C
ATOM 50 HB3 GLU A 4 28.209 14.877 8.613 1.00 0.00 H
ATOM 51 HB2 GLU A 4 28.927 13.570 9.734 1.00 0.00 H
ATOM 52 CG GLU A 4 30.400 15.140 9.010 1.00 0.00 C
ATOM 53 HG3 GLU A 4 31.338 14.917 9.713 1.00 0.00 H
ATOM 54 HG2 GLU A 4 30.559 16.245 8.583 1.00 0.00 H
ATOM 55 CD GLU A 4 30.820 14.370 7.750 1.00 0.00 C
ATOM 56 OE1 GLU A 4 31.770 13.490 7.830 1.00 0.00 O
ATOM 57 OE2 GLU A 4 30.220 14.580 6.660 1.00 0.00 O
ATOM 58 C GLU A 4 27.080 15.870 10.880 1.00 0.00 C
ATOM 59 O GLU A 4 26.440 16.810 10.390 1.00 0.00 O
ATOM 60 OXT GLU A 4 26.692 14.850 11.569 1.00 0.00 O
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