Skip to content

GitLab

Commit cbbc7911 authored by huangj's avatar huangj
Browse files

Update the cgenff parameters files in tests/systems from version 3.1 to 4.1

parent 9924e408
Expand all Show whitespace changes
Inline Side-by-side
Showing with 3478 additions and 751 deletions
wrappers/python/tests/TestCharmmFiles.py
View file @ cbbc7911
......@@ -116,8 +116,8 @@ class TestCharmmFiles(unittest.TestCase):
ene = state.getPotentialEnergy().value_in_unit(kilocalories_per_mole)
self.assertAlmostEqual(ene, 15490.0033559, delta=0.05)
def test_drude(self):
"""Tests CHARMM systems with Drude force field"""
def test_Drude(self):
"""Test CHARMM systems with Drude force field"""
warnings.filterwarnings('ignore', category=CharmmPSFWarning)
psf = CharmmPsfFile('systems/ala3_solv_drude.psf')
crd = CharmmCrdFile('systems/ala3_solv_drude.crd')
......@@ -136,6 +136,23 @@ class TestCharmmFiles(unittest.TestCase):
ene = state.getPotentialEnergy().value_in_unit(kilocalories_per_mole)
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):
""" Test the parsing of PSF files that contain insertion codes in their residue numbers """
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
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment