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Commit cbbc7911 authored by huangj's avatar huangj
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Update the cgenff parameters files in tests/systems from version 3.1 to 4.1

parent 9924e408
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Showing with 3478 additions and 751 deletions
wrappers/python/tests/TestCharmmFiles.py
View file @ cbbc7911
...@@ -116,8 +116,8 @@ class TestCharmmFiles(unittest.TestCase): ...@@ -116,8 +116,8 @@ class TestCharmmFiles(unittest.TestCase):
ene = state.getPotentialEnergy().value_in_unit(kilocalories_per_mole) ene = state.getPotentialEnergy().value_in_unit(kilocalories_per_mole)
self.assertAlmostEqual(ene, 15490.0033559, delta=0.05) self.assertAlmostEqual(ene, 15490.0033559, delta=0.05)
def test_drude(self): def test_Drude(self):
"""Tests CHARMM systems with Drude force field""" """Test CHARMM systems with Drude force field"""
warnings.filterwarnings('ignore', category=CharmmPSFWarning) warnings.filterwarnings('ignore', category=CharmmPSFWarning)
psf = CharmmPsfFile('systems/ala3_solv_drude.psf') psf = CharmmPsfFile('systems/ala3_solv_drude.psf')
crd = CharmmCrdFile('systems/ala3_solv_drude.crd') crd = CharmmCrdFile('systems/ala3_solv_drude.crd')
...@@ -136,6 +136,23 @@ class TestCharmmFiles(unittest.TestCase): ...@@ -136,6 +136,23 @@ class TestCharmmFiles(unittest.TestCase):
ene = state.getPotentialEnergy().value_in_unit(kilocalories_per_mole) ene = state.getPotentialEnergy().value_in_unit(kilocalories_per_mole)
self.assertAlmostEqual(ene, -1831.54, delta=0.5) self.assertAlmostEqual(ene, -1831.54, delta=0.5)
def test_Lonepair(self):
"""Test the lonepair facilities, in particular the colinear type of lonepairs"""
warnings.filterwarnings('ignore', category=CharmmPSFWarning)
psf = CharmmPsfFile('systems/chlb_cgenff.psf')
crd = CharmmCrdFile('systems/chlb_cgenff.crd')
# move the position of the lonepair on Cholride
params = CharmmParameterSet('systems/par_all36_cgenff.prm',
'systems/top_all36_cgenff.rtf')
# Box dimensions (found from bounding box)
plat = Platform.getPlatformByName('Reference')
system = psf.createSystem(params, nonbondedMethod=PME,
nonbondedCutoff=8*angstroms)
con = Context(system, VerletIntegrator(2*femtoseconds), plat)
con.setPositions(crd.positions)
def test_InsCode(self): def test_InsCode(self):
""" Test the parsing of PSF files that contain insertion codes in their residue numbers """ """ Test the parsing of PSF files that contain insertion codes in their residue numbers """
psf = CharmmPsfFile('systems/4TVP-dmj_wat-ion.psf') psf = CharmmPsfFile('systems/4TVP-dmj_wat-ion.psf')
......
wrappers/python/tests/systems/chlb_cgenff.crd 0 → 100644
View file @ cbbc7911
* GENERATE CPD ACCORDING TO IC TABLES IN FF
* USAGE: RUNCHM READ RESNAME= SEED= FF= ARHL=
* DATE: 6/14/19 14:22:39 CREATED BY USER: xu
*
13 EXT
1 1 CHLB C1 1.3878616207 -0.0212925645 0.0000000000 CHLB 1 -0.1000000000
2 1 CHLB H1 1.9158187876 -0.9626017904 0.0000000000 CHLB 1 0.1500000000
3 1 CHLB C2 2.0909297432 1.1920897951 -0.0000000000 CHLB 1 -0.1150000000
4 1 CHLB H2 3.1713458379 1.1910776735 -0.0000000000 CHLB 1 0.1150000000
5 1 CHLB C3 1.3891041046 2.4061558141 -0.0000000000 CHLB 1 -0.1150000000
6 1 CHLB H3 1.9293927824 3.3420080347 -0.0000000000 CHLB 1 0.1150000000
7 1 CHLB C4 -0.0132207406 2.4068634907 -0.0000000000 CHLB 1 -0.1150000000
8 1 CHLB H4 -0.5543440865 3.3420028049 -0.0000000000 CHLB 1 0.1150000000
9 1 CHLB C5 -0.7124562630 1.1912684987 0.0000000000 CHLB 1 -0.1000000000
10 1 CHLB H5 -1.7916319741 1.1777934579 0.0000000000 CHLB 1 0.1500000000
11 1 CHLB C6 -0.0118030037 -0.0204026447 0.0000000000 CHLB 1 0.0600000000
12 1 CHLB CL -0.8809968380 -1.5259625634 0.0000000000 CHLB 1 -0.2100000000
13 1 CHLB LP -1.7009674118 -2.9462612145 0.0000000000 CHLB 1 0.0500000000
wrappers/python/tests/systems/chlb_cgenff.psf 0 → 100644
View file @ cbbc7911
PSF EXT CMAP CHEQ XPLOR
3 !NTITLE
* GENERATE CPD ACCORDING TO IC TABLES IN FF
* USAGE: RUNCHM READ RESNAME= SEED= FF= ARHL=
* DATE: 6/14/19 14:22:39 CREATED BY USER: xu
13 !NATOM
1 CHLB 1 CHLB C1 CG2R61 -0.100000 12.0110 0 0.00000 -0.301140E-02
2 CHLB 1 CHLB H1 HGR62 0.150000 1.00800 0 0.00000 -0.301140E-02
3 CHLB 1 CHLB C2 CG2R61 -0.115000 12.0110 0 0.00000 -0.301140E-02
4 CHLB 1 CHLB H2 HGR61 0.115000 1.00800 0 0.00000 -0.301140E-02
5 CHLB 1 CHLB C3 CG2R61 -0.115000 12.0110 0 0.00000 -0.301140E-02
6 CHLB 1 CHLB H3 HGR61 0.115000 1.00800 0 0.00000 -0.301140E-02
7 CHLB 1 CHLB C4 CG2R61 -0.115000 12.0110 0 0.00000 -0.301140E-02
8 CHLB 1 CHLB H4 HGR61 0.115000 1.00800 0 0.00000 -0.301140E-02
9 CHLB 1 CHLB C5 CG2R61 -0.100000 12.0110 0 0.00000 -0.301140E-02
10 CHLB 1 CHLB H5 HGR62 0.150000 1.00800 0 0.00000 -0.301140E-02
11 CHLB 1 CHLB C6 CG2R61 0.600000E-01 12.0110 0 0.00000 -0.301140E-02
12 CHLB 1 CHLB CL CLGR1 -0.210000 35.4530 0 0.00000 -0.301140E-02
13 CHLB 1 CHLB LP LPH 0.500000E-01 0.00000 -1 0.00000 -0.301140E-02
13 !NBOND: bonds
1 2 1 3 3 4 3 5
5 6 5 7 7 8 7 9
9 10 9 11 11 1 11 12
12 13
18 !NTHETA: angles
2 1 3 2 1 11 3 1 11
1 3 4 1 3 5 4 3 5
3 5 6 3 5 7 6 5 7
5 7 8 5 7 9 8 7 9
7 9 10 7 9 11 10 9 11
1 11 9 1 11 12 9 11 12
24 !NPHI: dihedrals
1 3 5 6 1 3 5 7
1 11 9 7 1 11 9 10
2 1 3 4 2 1 3 5
2 1 11 9 2 1 11 12
3 1 11 9 3 1 11 12
3 5 7 8 3 5 7 9
4 3 1 11 4 3 5 6
4 3 5 7 5 3 1 11
5 7 9 10 5 7 9 11
6 5 7 8 6 5 7 9
7 9 11 12 8 7 9 10
8 7 9 11 10 9 11 12
0 !NIMPHI: impropers
0 !NDON: donors
0 !NACC: acceptors
0 !NNB
0 0 0 0 0 0 0 0
0 0 0 0 0
1 0 !NGRP NST2
0 1 0
1 !MOLNT
1 1 1 1 1 1 1 1
1 1 1 1 1
1 3 !NUMLP NUMLPH
2 1 F 1.64000 0.00000 0.00000
13 12 11
0 !NCRTERM: cross-terms
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