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Unverified Commit 44524bd1 authored by feiglab's avatar feiglab Committed by GitHub
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NBFIX in Gromacs for 1-4 pairs (#5050) 

* fix to correctly read Gromacs topology files for CHARMM force field

* updated fix to correctly read topology files with NBFIX and different combination rules

* fixes to read topology files with NBFIX and different combination rules

* changed default for useDispersionCorrection to True

* changed docstring default for useDispersionCorrection to 'True'

* fix scaling of 1-4 LJ pairs when NBFIX is used

* apply NBFIXes to 1-4 pairs if no pair parameters are given

* rerun CI
parent 1b6236a8
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Showing with 1084 additions and 14 deletions
wrappers/python/openmm/app/gromacstopfile.py
View file @ 44524bd1
......@@ -1148,21 +1148,30 @@ class GromacsTopFile(object):
key = min((tor[0], tor[3]),
(tor[3], tor[0]))
if key in excluded_atom_pairs: continue # multiterm...
q1 = atom_charges[tor[0]]
q4 = atom_charges[tor[3]]
charge_prod = fudgeQQ*q1*q4
try:
# use NBFix for 1-4 interactions if available to match GROMACS
types = self._matchingNBFIX[tuple(sorted((atom_types[tor[0]],atom_types[tor[3]])))]
params = (float(types[3]), float(types[4]))
rmin14=params[0]
epsilon=params[1]*fudgeLJ
except KeyError:
params1 = self._atomTypes[atom_types[tor[0]]]
params4 = self._atomTypes[atom_types[tor[3]]]
q1 = atom_charges[tor[0]]
rmin1 = float(params1[6])
eps1 = float(params1[7])
q4 = atom_charges[tor[3]]
rmin4 = float(params4[6])
eps4 = float(params4[7])
charge_prod = fudgeQQ*q1*q4
epsilon = math.sqrt(abs(eps1 * eps4))*fudgeLJ
if self._defaults[1] == '2':
rmin14 = (rmin1 + rmin4) / 2
else:
rmin14 = math.sqrt(rmin1 * rmin4)
# Parameters are generated via standard combining rules.
# If different 1-4 parameters are given via pairtypes they will be overwritten below.
if self._defaults[1] == '3':
......@@ -1194,7 +1203,7 @@ class GromacsTopFile(object):
nb.addException(exclusion[0], exclusion[1], 0.0, 1.0, 0.0, True)
# this will overwrite the pairs from the pairlist
# if nbfix, this will only overwrite paris if we have pairtype parameters
# if nbfix, this will only overwrite pairs if we have pairtype parameters
for pair in pairs:
nb.addException(pair[0], pair[1], pair[2], pair[3], pair[4], True)
......
wrappers/python/tests/TestGromacsTopFile.py
View file @ 44524bd1
......@@ -288,7 +288,8 @@ class TestGromacsTopFile(unittest.TestCase):
'apgr.nonbfix.nopairs.comb1.top': -918.572,
'apgr.nonbfix.nopairs.comb2.top': -909.637,
'apgr.nonbfix.nopairs.comb3.top': -918.572,
'apgr.nbfix.nopairs.comb2.fudge.top': -856.721
'apgr.nbfix.nopairs.comb2.fudge.top': -856.721,
'apgr.nbfix14.nopairs.comb2.top': -909.755
}
for topfile, expected in energies.items():
......
wrappers/python/tests/systems/apgr.nbfix14.nopairs.comb2.top 0 → 100644
View file @ 44524bd1
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 1.0 1.0
[ atomtypes ]
H 1 1.008000 0.000 A 0.040001352445 0.1924640
HA 1 1.008000 0.000 A 0.235197261589 0.0920480
HA2 1 1.008000 0.000 A 0.238760856462 0.1422560
HA3 1 1.008000 0.000 A 0.238760856462 0.1004160
HB1 1 1.008000 0.000 A 0.235197261589 0.0920480
HB2 1 1.008000 0.000 A 0.238760856462 0.1171520
HC 1 1.008000 0.000 A 0.040001352445 0.1924640
C 6 12.011000 0.000 A 0.356359487256 0.4602400
CC 6 12.011000 0.000 A 0.356359487256 0.2928800
CP1 6 12.011000 0.000 A 0.405358916754 0.0836800
CP2 6 12.011000 0.000 A 0.387540942391 0.2301200
CP3 6 12.011000 0.000 A 0.387540942391 0.2301200
CT1 6 12.011000 0.000 A 0.356359487256 0.1338880
CT2 6 12.011000 0.000 A 0.358141284692 0.2343040
CT3 6 12.011000 0.000 A 0.363486677001 0.3263520
N 7 14.007000 0.000 A 0.329632525712 0.8368000
NC2 7 14.007000 0.000 A 0.329632525712 0.8368000
NH1 7 14.007000 0.000 A 0.329632525712 0.8368000
NH3 7 14.007000 0.000 A 0.329632525712 0.8368000
O 8 15.999400 0.000 A 0.302905564168 0.5020800
OC 8 15.999400 0.000 A 0.302905564168 0.5020800
[ bondtypes ]
CP1 C 1 0.14900000 209200.00
CP1 CC 1 0.14900000 209200.00
CP2 CP1 1 0.15270000 186188.00
CP2 CP2 1 0.15370000 186188.00
CP3 CP2 1 0.15370000 186188.00
CT1 C 1 0.14900000 209200.00
CT1 CC 1 0.15220000 167360.00
CT1 CT1 1 0.15000000 186188.00
CT2 C 1 0.14900000 209200.00
CT2 CC 1 0.15220000 167360.00
CT2 CT1 1 0.15380000 186188.00
CT2 CT2 1 0.15300000 186188.00
CT3 C 1 0.14900000 209200.00
CT3 CC 1 0.15220000 167360.00
CT3 CT1 1 0.15380000 186188.00
CT3 CT2 1 0.15280000 186188.00
CT3 CT3 1 0.15300000 186188.00
HA2 CP2 1 0.11110000 258571.20
HA2 CP3 1 0.11110000 258571.20
HA2 CT2 1 0.11110000 258571.20
HA3 CT3 1 0.11110000 269449.60
HB1 CP1 1 0.10800000 276144.00
HB1 CT1 1 0.10800000 276144.00
HB2 CT2 1 0.10800000 276144.00
N C 1 0.13000000 217568.00
N CP1 1 0.14340000 267776.00
N CP3 1 0.14550000 267776.00
NC2 C 1 0.13650000 376560.00
NC2 CT2 1 0.14900000 326352.00
NC2 CT3 1 0.14900000 326352.00
NC2 HC 1 0.10000000 380744.00
NH1 C 1 0.13450000 309616.00
NH1 CT1 1 0.14300000 267776.00
NH1 CT2 1 0.14300000 267776.00
NH1 CT3 1 0.14300000 267776.00
NH1 H 1 0.09970000 368192.00
NH1 HC 1 0.09800000 338904.00
NH3 CT1 1 0.14800000 167360.00
NH3 CT2 1 0.14800000 167360.00
NH3 CT3 1 0.14800000 167360.00
NH3 HC 1 0.10400000 337230.40
O C 1 0.12300000 518816.00
O CC 1 0.12300000 543920.00
OC CC 1 0.12600000 439320.00
OC CT2 1 0.13300000 376560.00
OC CT3 1 0.13300000 376560.00
[ angletypes ]
HB2 CT1 HB2 5 115.000000 301.248000 0.00000000 0.00
NH1 CT1 HB2 5 108.000000 401.664000 0.00000000 0.00
CP1 N C 5 117.000000 502.080000 0.00000000 0.00
CP2 CP1 C 5 112.300000 435.136000 0.00000000 0.00
CP2 CP1 CC 5 112.300000 435.136000 0.00000000 0.00
CP2 CP2 CP1 5 108.500000 585.760000 0.00000000 0.00
CP3 CP2 CP2 5 108.500000 585.760000 0.00000000 0.00
CP3 N C 5 117.000000 502.080000 0.00000000 0.00
CP3 N CP1 5 114.200000 836.800000 0.00000000 0.00
CT1 CT1 C 5 108.000000 435.136000 0.00000000 0.00
CT1 CT1 CC 5 108.000000 435.136000 0.00000000 0.00
CT1 CT1 CT1 5 111.000000 446.432800 0.25610000 6694.40
CT1 CT2 CC 5 108.000000 435.136000 0.00000000 0.00
CT1 CT2 CT1 5 113.500000 488.272800 0.25610000 9338.69
CT1 NH1 C 5 120.000000 418.400000 0.00000000 0.00
CT2 CT1 C 5 108.000000 435.136000 0.00000000 0.00
CT2 CT1 CC 5 108.000000 435.136000 0.00000000 0.00
CT2 CT1 CT1 5 111.000000 446.432800 0.25610000 6694.40
CT2 CT2 C 5 108.000000 435.136000 0.00000000 0.00
CT2 CT2 CC 5 108.000000 435.136000 0.00000000 0.00
CT3 CT2 CC 5 108.000000 435.136000 0.00000000 0.00
CT2 CT2 CT1 5 113.500000 488.272800 0.25610000 9338.69
CT2 CT2 CT2 5 113.600000 488.272800 0.25610000 9338.69
CT2 CT3 CT1 5 113.500000 488.272800 0.25610000 9338.69
CT2 NC2 C 5 120.000000 521.326400 0.00000000 0.00
CT2 NH1 C 5 120.000000 418.400000 0.00000000 0.00
CT3 CT1 C 5 108.000000 435.136000 0.00000000 0.00
CT3 CT1 CC 5 108.000000 435.136000 0.00000000 0.00
CT3 CT1 CT1 5 108.500000 446.432800 0.25610000 6694.40
CT3 CT1 CT2 5 114.000000 446.432800 0.25610000 6694.40
CT3 CT1 CT3 5 114.000000 446.432800 0.25610000 6694.40
CT3 CT2 CT1 5 113.500000 488.272800 0.25610000 9338.69
CT3 CT2 CT2 5 115.000000 485.344000 0.25610000 6694.40
CT3 CT2 CT3 5 114.000000 446.432800 0.25610000 6694.40
CT3 NC2 C 5 120.000000 521.326400 0.00000000 0.00
CT3 NH1 C 5 120.000000 418.400000 0.00000000 0.00
H NH1 C 5 123.000000 284.512000 0.00000000 0.00
H NH1 CT1 5 117.000000 292.880000 0.00000000 0.00
H NH1 CT2 5 117.000000 292.880000 0.00000000 0.00
H NH1 CT3 5 117.000000 292.880000 0.00000000 0.00
HA2 CP2 CP1 5 110.100000 279.742240 0.21790000 18853.10
HA2 CP2 CP2 5 110.100000 221.752000 0.21790000 18853.10
HA2 CP2 CP3 5 110.100000 221.752000 0.21790000 18853.10
HA2 CP2 HA2 5 109.000000 297.064000 0.18020000 4518.72
HA2 CP3 CP2 5 110.100000 221.752000 0.21790000 18853.10
HA2 CP3 HA2 5 109.000000 297.064000 0.18020000 4518.72
HA2 CT2 C 5 109.500000 276.144000 0.21630000 25104.00
HA2 CT2 CC 5 109.500000 276.144000 0.21630000 25104.00
HA2 CT2 CT1 5 110.100000 221.752000 0.21790000 18853.10
HA2 CT2 CT2 5 110.100000 221.752000 0.21790000 18853.10
HA2 CT2 CT3 5 110.100000 289.532800 0.21790000 18853.10
HA2 CT2 HA2 5 109.000000 297.064000 0.18020000 4518.72
HA3 CT3 C 5 109.500000 276.144000 0.21630000 25104.00
HA3 CT3 CC 5 109.500000 276.144000 0.21630000 25104.00
HA3 CT3 CT1 5 110.100000 279.742240 0.21790000 18853.10
HA3 CT3 CT2 5 110.100000 289.532800 0.21790000 18853.10
HA3 CT3 CT3 5 110.100000 313.800000 0.21790000 18853.10
HA3 CT3 HA3 5 108.400000 297.064000 0.18020000 4518.72
HB1 CP1 C 5 112.000000 418.400000 0.00000000 0.00
HB1 CP1 CC 5 112.000000 418.400000 0.00000000 0.00
HB1 CP1 CP2 5 118.000000 292.880000 0.00000000 0.00
HB1 CT1 C 5 109.500000 418.400000 0.00000000 0.00
HB1 CT1 CC 5 109.500000 418.400000 0.00000000 0.00
HB1 CT1 CT1 5 111.000000 292.880000 0.00000000 0.00
HB1 CT1 CT2 5 111.000000 292.880000 0.00000000 0.00
HB1 CT1 CT3 5 111.000000 292.880000 0.00000000 0.00
HB2 CT2 C 5 109.500000 418.400000 0.00000000 0.00
HB2 CT2 CC 5 109.500000 418.400000 0.00000000 0.00
HB2 CT2 HB2 5 115.000000 301.248000 0.00000000 0.00
HC NC2 C 5 120.000000 410.032000 0.00000000 0.00
HC NC2 CT2 5 120.000000 338.067200 0.00000000 0.00
HC NC2 CT3 5 120.000000 338.067200 0.00000000 0.00
HC NC2 HC 5 120.000000 209.200000 0.00000000 0.00
HC NH3 CT1 5 109.500000 251.040000 0.20740000 16736.00
HC NH3 CT2 5 109.500000 251.040000 0.20740000 16736.00
HC NH3 CT3 5 109.500000 251.040000 0.20740000 16736.00
HC NH3 HC 5 109.500000 368.192000 0.00000000 0.00
N C CP1 5 112.500000 167.360000 0.00000000 0.00
N C CT1 5 112.500000 167.360000 0.00000000 0.00
N C CT2 5 112.500000 167.360000 0.00000000 0.00
N C CT3 5 112.500000 167.360000 0.00000000 0.00
N CP1 C 5 108.200000 418.400000 0.00000000 0.00
N CP1 CC 5 108.200000 418.400000 0.00000000 0.00
N CP1 CP2 5 110.800000 585.760000 0.00000000 0.00
N CP1 HB1 5 112.000000 401.664000 0.00000000 0.00
N CP3 CP2 5 110.500000 585.760000 0.00000000 0.00
N CP3 HA2 5 108.000000 401.664000 0.00000000 0.00
NC2 C NC2 5 120.000000 334.720000 0.23100000 58576.00 ;
NC2 CT2 CT2 5 107.500000 566.513600 0.00000000 0.00
NC2 CT2 HA2 5 107.500000 472.792000 0.00000000 0.00
NC2 CT3 HA3 5 107.500000 472.792000 0.00000000 0.00
NH1 C CP1 5 116.500000 669.440000 0.00000000 0.00
NH1 C CT1 5 116.500000 669.440000 0.00000000 0.00
NH1 C CT2 5 116.500000 669.440000 0.00000000 0.00
NH1 C CT3 5 116.500000 669.440000 0.00000000 0.00
NH1 CT1 C 5 107.000000 418.400000 0.00000000 0.00
NH1 CT1 CC 5 107.000000 418.400000 0.00000000 0.00
NH1 CT1 CT1 5 113.500000 585.760000 0.00000000 0.00
NH1 CT1 CT2 5 113.500000 585.760000 0.00000000 0.00
NH1 CT1 CT3 5 113.500000 585.760000 0.00000000 0.00
NH1 CT1 HB1 5 108.000000 401.664000 0.00000000 0.00
NH1 CT2 C 5 107.000000 418.400000 0.00000000 0.00
NH1 CT2 CC 5 107.000000 418.400000 0.00000000 0.00
NH1 CT2 CT2 5 113.500000 585.760000 0.00000000 0.00
NH1 CT2 HA2 5 109.500000 430.952000 0.00000000 0.00
NH1 CT2 HB2 5 108.000000 401.664000 0.00000000 0.00
NH1 CT3 HA3 5 109.500000 430.952000 0.00000000 0.00
NH3 CT1 C 5 110.000000 365.681600 0.00000000 0.00
NH3 CT1 CC 5 110.000000 365.681600 0.00000000 0.00
NH3 CT1 CT1 5 110.000000 566.513600 0.00000000 0.00
NH3 CT1 CT2 5 110.000000 566.513600 0.00000000 0.00
NH3 CT1 CT3 5 110.000000 566.513600 0.00000000 0.00
NH3 CT1 HB1 5 107.500000 430.952000 0.00000000 0.00
NH3 CT2 C 5 110.000000 365.681600 0.00000000 0.00
NH3 CT2 CC 5 110.000000 365.681600 0.00000000 0.00
NH3 CT2 CT2 5 110.000000 566.513600 0.00000000 0.00
NH3 CT2 CT3 5 110.000000 566.513600 0.00000000 0.00
NH3 CT2 HA2 5 107.500000 376.560000 0.21010000 29288.00
NH3 CT2 HB2 5 107.500000 430.952000 0.00000000 0.00
NH3 CT3 HA3 5 107.500000 376.560000 0.21010000 29288.00
O C CP1 5 118.000000 669.440000 0.00000000 0.00
O C CT1 5 121.000000 669.440000 0.00000000 0.00
O C CT2 5 121.000000 669.440000 0.00000000 0.00
O C CT3 5 121.000000 669.440000 0.00000000 0.00
O C H 5 121.700000 418.400000 0.00000000 0.00
O C N 5 122.500000 669.440000 0.00000000 0.00
O C NH1 5 122.500000 669.440000 0.00000000 0.00
O CC CP1 5 118.000000 669.440000 0.00000000 0.00
O CC CT1 5 121.000000 125.520000 0.24400000 41840.00
O CC CT2 5 121.000000 125.520000 0.24400000 41840.00
O CC CT3 5 121.000000 125.520000 0.24400000 41840.00
OC CC CP1 5 118.000000 334.720000 0.23880000 41840.00
OC CC CT1 5 118.000000 334.720000 0.23880000 41840.00
OC CC CT2 5 118.000000 334.720000 0.23880000 41840.00
OC CC CT3 5 118.000000 334.720000 0.23880000 41840.00
OC CC OC 5 124.000000 836.800000 0.22250000 58576.00
OC CT2 CT3 5 122.000000 543.920000 0.00000000 0.00
OC CT2 HA2 5 118.300000 543.920000 0.00000000 0.00
OC CT3 HA3 5 118.300000 543.920000 0.00000000 0.00
OC CT2 CT1 5 122.000000 543.920000 0.00000000 0.00
[ dihedraltypes ]
C CT1 NH1 C 9 180.000000 0.836800 1
C CT2 NH1 C 9 180.000000 0.836800 1
C N CP1 C 9 0.000000 3.347200 3
CC CP1 N C 9 0.000000 3.347200 3
CC CT1 NH1 C 9 180.000000 0.836800 1
CC CT2 NH1 C 9 180.000000 8.368000 1
CP1 C N CP1 9 180.000000 11.506000 2
CP1 C N CP1 9 0.000000 1.255200 4
CP2 CP1 N C 9 0.000000 3.347200 3
CP2 CP3 N C 9 180.000000 0.000000 3
CP2 CP3 N CP1 9 0.000000 0.418400 3
CP3 N C CP1 9 180.000000 11.506000 2
CP3 N C CP1 9 0.000000 1.255200 4
CP3 N CP1 C 9 0.000000 0.418400 3
CP3 N CP1 CC 9 0.000000 0.418400 3
CP3 N CP1 CP2 9 0.000000 0.418400 3
CT1 C N CP1 9 180.000000 11.506000 2
CT1 C N CP1 9 0.000000 1.255200 4
CT1 C N CP3 9 180.000000 11.506000 2
CT1 C N CP3 9 0.000000 1.255200 4
CT1 C NH1 CT1 9 0.000000 6.694400 1
CT1 C NH1 CT1 9 180.000000 10.460000 2
CT1 CT1 NH1 C 9 0.000000 7.531200 1
CT1 NH1 C CP1 9 0.000000 6.694400 1
CT1 NH1 C CP1 9 180.000000 10.460000 2
CT2 C N CP1 9 180.000000 11.506000 2
CT2 C N CP1 9 0.000000 1.255200 4
CT2 C N CP3 9 180.000000 11.506000 2
CT2 C N CP3 9 0.000000 1.255200 4
CT2 C NH1 CT1 9 0.000000 6.694400 1
CT2 C NH1 CT1 9 180.000000 10.460000 2
CT2 C NH1 CT2 9 0.000000 6.694400 1
CT2 C NH1 CT2 9 180.000000 10.460000 2
CT2 C NH1 CT3 9 0.000000 6.694400 1
CT2 C NH1 CT3 9 180.000000 10.460000 2
CT2 CT1 NH1 C 9 0.000000 7.531200 1
CT2 CT2 CT2 CT2 9 180.000000 0.418400 2
CT2 CT2 CT2 CT2 9 0.000000 0.627600 4
CT2 CT2 CT2 CT2 9 180.000000 0.418400 6
CT2 CT2 CT2 CT3 9 180.000000 0.418400 2
CT2 CT2 CT2 CT3 9 0.000000 0.627600 4
CT2 CT2 CT2 CT3 9 180.000000 0.418400 6
CT2 CT2 NH1 C 9 0.000000 7.531200 1
CT2 NH1 C CP1 9 0.000000 6.694400 1
CT2 NH1 C CP1 9 180.000000 10.460000 2
CT2 NH1 C CT1 9 0.000000 6.694400 1
CT2 NH1 C CT1 9 180.000000 10.460000 2
CT3 C N CP1 9 180.000000 11.506000 2
CT3 C N CP1 9 0.000000 1.255200 4
CT3 C N CP3 9 180.000000 11.506000 2
CT3 C N CP3 9 0.000000 1.255200 4
CT3 C NH1 CT1 9 0.000000 6.694400 1
CT3 C NH1 CT1 9 180.000000 10.460000 2
CT3 C NH1 CT2 9 0.000000 6.694400 1
CT3 C NH1 CT2 9 180.000000 10.460000 2
CT3 C NH1 CT3 9 0.000000 6.694400 1
CT3 C NH1 CT3 9 180.000000 10.460000 2
CT3 CT1 NH1 C 9 0.000000 7.531200 1
CT3 NH1 C CP1 9 0.000000 6.694400 1
CT3 NH1 C CP1 9 180.000000 10.460000 2
CT3 NH1 C CT1 9 0.000000 6.694400 1
CT3 NH1 C CT1 9 180.000000 10.460000 2
H NH1 C CP1 9 180.000000 10.460000 2
H NH1 C CT1 9 180.000000 10.460000 2
H NH1 C CT2 9 180.000000 10.460000 2
H NH1 C CT3 9 180.000000 10.460000 2
H NH1 CT1 C 9 0.000000 0.000000 1
H NH1 CT1 CC 9 0.000000 0.000000 1
H NH1 CT1 CT1 9 0.000000 0.000000 1
H NH1 CT1 CT2 9 0.000000 0.000000 1
H NH1 CT1 CT3 9 0.000000 0.000000 1
H NH1 CT2 C 9 0.000000 0.000000 1
H NH1 CT2 CC 9 0.000000 0.000000 1
H NH1 CT2 CT2 9 0.000000 0.000000 1
H NH1 CT2 CT3 9 0.000000 0.000000 1
HA2 CP3 N C 9 180.000000 0.000000 3
HA2 CP3 N CP1 9 0.000000 0.418400 3
HA2 CT2 NH1 C 9 0.000000 0.000000 3
HA2 CT2 NH1 H 9 0.000000 0.000000 3
HA3 CT3 NH1 C 9 0.000000 0.000000 3
HA3 CT3 NH1 H 9 0.000000 0.000000 3
HB1 CP1 N C 9 0.000000 3.347200 3
HB1 CP1 N CP3 9 0.000000 0.418400 3
HB1 CT1 NH1 C 9 0.000000 0.000000 1
HB1 CT1 NH1 H 9 0.000000 0.000000 1
HB2 CT2 NH1 C 9 0.000000 0.000000 1
HB2 CT2 NH1 H 9 0.000000 0.000000 1
N C CP1 CP2 9 0.000000 1.673600 1
N C CP1 CP2 9 0.000000 2.510400 2
N C CP1 HB1 9 180.000000 1.673600 1
N C CP1 HB1 9 0.000000 2.510400 2
N C CP1 N 9 0.000000 1.255200 1
N C CP1 N 9 0.000000 -1.255200 4
N C CT1 CT1 9 0.000000 0.000000 1
N C CT1 CT2 9 0.000000 0.000000 1
N C CT1 CT3 9 0.000000 0.000000 1
N C CT1 HB1 9 0.000000 0.000000 1
N C CT2 HB2 9 0.000000 0.000000 1
N C CT3 HA3 9 0.000000 0.000000 1
NH1 C CP1 CP2 9 0.000000 1.673600 1
NH1 C CP1 CP2 9 0.000000 2.510400 2
NH1 C CP1 HB1 9 180.000000 1.673600 1
NH1 C CP1 HB1 9 0.000000 2.510400 2
NH1 C CP1 N 9 0.000000 1.255200 1
NH1 C CP1 N 9 0.000000 -1.255200 4
NH1 C CT1 CT1 9 0.000000 0.000000 1
NH1 C CT1 CT2 9 0.000000 0.000000 1
NH1 C CT1 CT3 9 0.000000 0.000000 1
NH1 C CT1 HB1 9 0.000000 0.000000 1
NH1 C CT1 NH1 9 0.000000 2.510400 1
NH1 C CT2 CT2 9 0.000000 0.000000 1
NH1 C CT2 HA2 9 0.000000 0.000000 3
NH1 C CT2 HB2 9 0.000000 0.000000 1
NH1 C CT2 NH1 9 0.000000 2.510400 1
NH1 C CT3 HA3 9 0.000000 0.000000 3
NH1 CT1 C N 9 0.000000 1.673600 1
NH1 CT2 C N 9 0.000000 1.673600 1
NH3 CT1 C N 9 0.000000 1.673600 1
NH3 CT1 C NH1 9 0.000000 2.510400 1
NH3 CT2 C N 9 0.000000 1.673600 1
NH3 CT2 C NH1 9 0.000000 4.184000 1
O C CP1 CP2 9 180.000000 1.673600 1
O C CP1 CP2 9 0.000000 2.510400 2
O C CP1 HB1 9 0.000000 1.673600 1
O C CP1 HB1 9 0.000000 2.510400 2
O C CP1 N 9 0.000000 -1.255200 4
O C CT1 CT1 9 0.000000 5.857600 1
O C CT1 CT2 9 0.000000 5.857600 1
O C CT1 CT3 9 0.000000 5.857600 1
O C CT1 HB1 9 0.000000 0.000000 1
O C CT1 NH1 9 0.000000 0.000000 1
O C CT1 NH3 9 0.000000 0.000000 1
O C CT2 CT2 9 0.000000 5.857600 1
O C CT2 HA2 9 180.000000 0.000000 3
O C CT2 HB2 9 0.000000 0.000000 1
O C CT2 NH1 9 0.000000 0.000000 1
O C CT2 NH3 9 0.000000 0.000000 1
O C CT3 HA3 9 180.000000 0.000000 3
O C N CP1 9 180.000000 11.506000 2
O C N CP1 9 0.000000 1.255200 4
O C N CP3 9 180.000000 11.506000 2
O C N CP3 9 0.000000 1.255200 4
O C NH1 CT1 9 180.000000 10.460000 2
O C NH1 CT2 9 180.000000 10.460000 2
O C NH1 CT3 9 180.000000 10.460000 2
O C NH1 H 9 180.000000 10.460000 2
O CC CP1 CP2 9 180.000000 1.673600 1
O CC CP1 CP2 9 0.000000 2.510400 2
O CC CP1 HB1 9 0.000000 1.673600 1
O CC CP1 HB1 9 0.000000 2.510400 2
O CC CP1 N 9 0.000000 -1.255200 4
O CC CT2 HA2 9 180.000000 0.000000 3
OC CC CP1 CP2 9 0.000000 0.669440 3
OC CC CP1 HB1 9 0.000000 0.669440 3
OC CC CP1 N 9 0.000000 0.669440 3
OC CC CT1 NH3 9 180.000000 13.388800 2
OC CC CT2 NH3 9 180.000000 13.388800 2
HB1 CT1 CT1 CT3 9 0.000000 0.836800 3
NH1 CT1 CT2 HA2 9 0.000000 0.836800 3
HB1 CT1 CT2 HA2 9 0.000000 0.836800 3
HB1 CT1 CT2 CT2 9 0.000000 0.836800 3
HA2 CT2 CT1 C 9 0.000000 0.836800 3
CT1 CT2 CT2 HA2 9 0.000000 0.794960 3
HA2 CT2 CT2 HA2 9 0.000000 0.794960 3
HA2 CT2 CT2 CC 9 0.000000 0.794960 3
CT2 CT2 CT2 HA2 9 0.000000 0.794960 3
CT2 CT2 CT2 NC2 9 0.000000 0.794960 3
CT2 CT2 NC2 HC 9 180.000000 0.000000 6
CT2 CT2 NC2 C 9 180.000000 0.000000 6
HA2 CT2 CT2 NC2 9 0.000000 0.794960 3
CT2 NC2 C NC2 9 180.000000 9.414000 2
HA2 CT2 NC2 HC 9 180.000000 0.000000 6
HA2 CT2 NC2 C 9 180.000000 0.000000 6
NC2 C NC2 HC 9 180.000000 9.414000 2
HB1 CT1 CT2 CC 9 0.000000 0.836800 3
HA2 CT2 CC OC 9 180.000000 0.209200 6
CT1 CT1 CT3 HA3 9 0.000000 0.836800 3
CT1 CT1 CT2 HA2 9 0.000000 0.836800 3
HB1 CT1 CT1 CT2 9 0.000000 0.836800 3
CT1 CT2 CT3 HA3 9 0.000000 0.669440 3
CT3 CT1 CT2 HA2 9 0.000000 0.836800 3
CT3 CT1 CT2 CT3 9 0.000000 0.836800 3
HA3 CT3 CT1 CT2 9 0.000000 0.836800 3
HA2 CT2 CT3 HA3 9 0.000000 0.669440 3
HB1 CT1 CT2 CT1 9 0.000000 0.836800 3
CT3 CT1 CT3 HA3 9 0.000000 0.836800 3
CT2 CT2 CT2 NH3 9 0.000000 0.794960 3
CT2 CT2 NH3 HC 9 0.000000 0.418400 3
HA2 CT2 CT2 NH3 9 0.000000 0.794960 3
HA2 CT2 NH3 HC 9 0.000000 0.418400 3
CT2 CT2 CC O 9 180.000000 0.209200 6
CT2 CT2 CC OC 9 180.000000 0.209200 6
C CT1 CT2 CT2 9 180.000000 1.464400 1 ;
C CT1 CT2 CT2 9 180.000000 1.757280 2 ;
C CT1 CT2 CT2 9 180.000000 7.991440 3 ;
CT2 CT2 CT1 NH1 9 180.000000 3.681920 1 ;
CT2 CT2 CT1 NH1 9 180.000000 0.000000 2 ;
CT2 CT2 CT1 NH1 9 0.000000 7.949600 3 ;
CC CT2 CT2 CT1 9 180.000000 7.698560 1 ;
CC CT2 CT2 CT1 9 180.000000 3.514560 2 ;
CC CT2 CT2 CT1 9 180.000000 1.631760 3 ;
CT1 CT2 CT2 CT2 9 180.000000 2.635920 1 ;
CT1 CT2 CT2 CT2 9 0.000000 0.041840 2 ;
CT1 CT2 CT2 CT2 9 0.000000 0.627600 3 ;
C CT1 CT2 CC 9 180.000000 5.899440 1 ;
C CT1 CT2 CC 9 180.000000 5.397360 2 ;
C CT1 CT2 CC 9 180.000000 2.468560 3 ;
CC CT2 CT1 NH1 9 180.000000 1.171520 1 ;
CC CT2 CT1 NH1 9 180.000000 2.092000 2 ;
CC CT2 CT1 NH1 9 0.000000 1.589920 3 ;
CT1 CT2 CC O 9 180.000000 1.757280 1 ;
CT1 CT2 CC O 9 180.000000 0.627600 2 ;
CT1 CT2 CC O 9 180.000000 3.974800 3 ;
CT1 CT1 CT2 CT3 9 180.000000 1.589920 1 ;
CT1 CT1 CT2 CT3 9 180.000000 0.543920 2 ;
CT1 CT1 CT2 CT3 9 180.000000 1.213360 3 ;
C CT1 CT1 CT2 9 180.000000 0.418400 1 ;
C CT1 CT1 CT2 9 180.000000 2.175680 2 ;
C CT1 CT1 CT2 9 180.000000 1.213360 3 ;
CT2 CT1 CT1 NH1 9 180.000000 0.502080 1 ;
CT2 CT1 CT1 NH1 9 180.000000 1.506240 2 ;
CT2 CT1 CT1 NH1 9 0.000000 1.715440 3 ;
CT1 CT2 CT1 CT3 9 0.000000 0.209200 1 ;
CT1 CT2 CT1 CT3 9 180.000000 0.418400 2 ;
CT1 CT2 CT1 CT3 9 180.000000 0.041840 3 ;
C CT1 CT2 CT1 9 180.000000 1.338880 1 ;
C CT1 CT2 CT1 9 180.000000 2.552240 2 ;
C CT1 CT2 CT1 9 180.000000 3.012480 3 ;
CT1 CT2 CT1 NH1 9 180.000000 2.008320 1 ;
CT1 CT2 CT1 NH1 9 180.000000 1.757280 2 ;
CT1 CT2 CT1 NH1 9 0.000000 2.719600 3 ;
C CT1 CT1 CT3 9 180.000000 0.585760 1 ;
C CT1 CT1 CT3 9 180.000000 1.087840 2 ;
C CT1 CT1 CT3 9 180.000000 1.380720 3 ;
CT3 CT1 CT1 NH1 9 0.000000 0.753120 1 ;
CT3 CT1 CT1 NH1 9 0.000000 0.251040 2 ;
CT3 CT1 CT1 NH1 9 0.000000 2.468560 3 ;
NH1 CT1 CT2 OC 9 0.000000 0.836800 3
NH3 CT1 CT2 OC 9 0.000000 0.836800 3
C CT1 CT2 OC 9 0.000000 0.836800 3
CC CT1 CT2 OC 9 0.000000 0.836800 3
HB1 CT1 CT2 OC 9 0.000000 0.836800 3
X C NC2 X 9 180.000000 9.414000 2
X CP1 C X 9 180.000000 0.000000 6
X CP1 CC X 9 180.000000 0.000000 6
X CP1 CP2 X 9 0.000000 0.585760 3
X CP2 CP2 X 9 0.000000 0.669440 3
X CP3 CP2 X 9 0.000000 0.585760 3
X CT1 CC X 9 180.000000 0.209200 6
X CT1 CT1 X 9 0.000000 0.836800 3
X CT1 CT2 X 9 0.000000 0.836800 3
X CT1 CT3 X 9 0.000000 0.836800 3
X CT1 NH3 X 9 0.000000 0.418400 3
X CT2 CC X 9 180.000000 0.209200 6
X CT2 CT2 X 9 0.000000 0.794960 3
X CT2 CT3 X 9 0.000000 0.669440 3
X CT2 NC2 X 9 180.000000 0.000000 6
X CT2 NH3 X 9 0.000000 0.418400 3
X CT3 CC X 9 180.000000 0.209200 6
X CT3 CT3 X 9 0.000000 0.638060 3
X CT3 NC2 X 9 180.000000 0.000000 6
X CT3 NH3 X 9 0.000000 0.376560 3
N C CP1 CP3 2 0.000000 0.000000
C HC HC NC2 2 0.000000 0.000000 ;
O N CT2 CC 2 0.000000 1004.160000
NC2 X X C 2 0.000000 376.560000
NC2 X X HC 2 0.000000 -16.736000 ;
NH1 X X H 2 0.000000 167.360000
O X X C 2 0.000000 1004.160000
OC X X CC 2 0.000000 803.328000
CC X X CT1 2 0.000000 803.328000
CC X X CT2 2 0.000000 803.328000
CC X X CT3 2 0.000000 803.328000
[ nonbond_params ]
H O 1 0.150 1.25
[ moleculetype ]
; Name nrexcl
Protein 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
; residue 1 ALA rtp ALA q +1.0
1 NH3 1 ALA N 1 -0.3 14.007
2 HC 1 ALA H1 2 0.33 1.008
3 HC 1 ALA H2 3 0.33 1.008
4 HC 1 ALA H3 4 0.33 1.008
5 CT1 1 ALA CA 5 0.21 12.011
6 HB1 1 ALA HA 5 0.1 1.008
7 CT3 1 ALA CB 6 -0.27 12.011
8 HA3 1 ALA HB1 6 0.09 1.008
9 HA3 1 ALA HB2 6 0.09 1.008
10 HA3 1 ALA HB3 6 0.09 1.008
11 C 1 ALA C 7 0.51 12.011
12 O 1 ALA O 7 -0.51 15.9994
; residue 2 PRO rtp PRO q 0.0
13 N 2 PRO N 8 -0.29 14.007
14 CP3 2 PRO CD 8 0 12.011
15 HA2 2 PRO HD1 8 0.09 1.008
16 HA2 2 PRO HD2 8 0.09 1.008
17 CP1 2 PRO CA 8 0.02 12.011
18 HB1 2 PRO HA 8 0.09 1.008
19 CP2 2 PRO CB 9 -0.18 12.011
20 HA2 2 PRO HB1 9 0.09 1.008
21 HA2 2 PRO HB2 9 0.09 1.008
22 CP2 2 PRO CG 10 -0.18 12.011
23 HA2 2 PRO HG1 10 0.09 1.008
24 HA2 2 PRO HG2 10 0.09 1.008
25 C 2 PRO C 11 0.51 12.011
26 O 2 PRO O 11 -0.51 15.9994
; residue 3 GLY rtp GLY q 0.0
27 NH1 3 GLY N 12 -0.47 14.007
28 H 3 GLY HN 12 0.31 1.008
29 CT2 3 GLY CA 12 -0.02 12.011
30 HB2 3 GLY HA1 12 0.09 1.008
31 HB2 3 GLY HA2 12 0.09 1.008
32 C 3 GLY C 13 0.51 12.011
33 O 3 GLY O 13 -0.51 15.9994
; residue 4 ARG rtp ARG q 0.0
34 NH1 4 ARG N 14 -0.47 14.007
35 H 4 ARG HN 14 0.31 1.008
36 CT1 4 ARG CA 14 0.07 12.011
37 HB1 4 ARG HA 14 0.09 1.008
38 CT2 4 ARG CB 15 -0.18 12.011
39 HA2 4 ARG HB1 15 0.09 1.008
40 HA2 4 ARG HB2 15 0.09 1.008
41 CT2 4 ARG CG 16 -0.18 12.011
42 HA2 4 ARG HG1 16 0.09 1.008
43 HA2 4 ARG HG2 16 0.09 1.008
44 CT2 4 ARG CD 17 0.2 12.011
45 HA2 4 ARG HD1 17 0.09 1.008
46 HA2 4 ARG HD2 17 0.09 1.008
47 NC2 4 ARG NE 17 -0.7 14.007
48 HC 4 ARG HE 17 0.44 1.008
49 C 4 ARG CZ 17 0.64 12.011
50 NC2 4 ARG NH1 17 -0.8 14.007
51 HC 4 ARG HH11 17 0.46 1.008
52 HC 4 ARG HH12 17 0.46 1.008
53 NC2 4 ARG NH2 17 -0.8 14.007
54 HC 4 ARG HH21 17 0.46 1.008
55 HC 4 ARG HH22 17 0.46 1.008
56 CC 4 ARG C 18 0.34 12.011
57 OC 4 ARG OT1 19 -0.67 15.9994
58 OC 4 ARG OT2 20 -0.67 15.9994
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 1
1 3 1
1 4 1
1 5 1
5 6 1
5 7 1
5 11 1
7 8 1
7 9 1
7 10 1
11 12 1
11 13 1
13 14 1
13 17 1
14 15 1
14 16 1
14 22 1
17 18 1
17 19 1
17 25 1
19 20 1
19 21 1
19 22 1
22 23 1
22 24 1
25 26 1
25 27 1
27 28 1
27 29 1
29 30 1
29 31 1
29 32 1
32 33 1
32 34 1
34 35 1
34 36 1
36 37 1
36 38 1
36 56 1
38 39 1
38 40 1
38 41 1
41 42 1
41 43 1
41 44 1
44 45 1
44 46 1
44 47 1
47 48 1
47 49 1
49 50 1
49 53 1
50 51 1
50 52 1
53 54 1
53 55 1
56 57 1
56 58 1
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 8 1
1 9 1
1 10 1
1 12 1
1 13 1
2 6 1
2 7 1
2 11 1
3 6 1
3 7 1
3 11 1
4 6 1
4 7 1
4 11 1
5 14 1
5 17 1
6 8 1
6 9 1
6 10 1
6 12 1
6 13 1
7 12 1
7 13 1
8 11 1
9 11 1
10 11 1
11 15 1
11 16 1
11 18 1
11 19 1
11 22 1
11 25 1
12 14 1
12 17 1
13 20 1
13 21 1
13 23 1
13 24 1
13 26 1
13 27 1
14 18 1
14 20 1
14 21 1
14 25 1
15 17 1
15 19 1
15 23 1
15 24 1
16 17 1
16 19 1
16 23 1
16 24 1
17 23 1
17 24 1
17 28 1
17 29 1
18 20 1
18 21 1
18 22 1
18 26 1
18 27 1
19 26 1
19 27 1
20 23 1
20 24 1
20 25 1
21 23 1
21 24 1
21 25 1
22 25 1
25 30 1
25 31 1
25 32 1
26 28 1
26 29 1
27 33 1
27 34 1
28 30 1
28 31 1
28 32 1
29 35 1
29 36 1
30 33 1
30 34 1
31 33 1
31 34 1
32 37 1
32 38 1
32 56 1
33 35 1
33 36 1
34 39 1
34 40 1
34 41 1
34 57 1
34 58 1
35 37 1
35 38 1
35 56 1
36 42 1
36 43 1
36 44 1
37 39 1
37 40 1
37 41 1
37 57 1
37 58 1
38 45 1
38 46 1
38 47 1
38 57 1
38 58 1
39 42 1
39 43 1
39 44 1
39 56 1
40 42 1
40 43 1
40 44 1
40 56 1
41 48 1
41 49 1
41 56 1
42 45 1
42 46 1
42 47 1
43 45 1
43 46 1
43 47 1
44 50 1
44 53 1
45 48 1
45 49 1
46 48 1
46 49 1
47 51 1
47 52 1
47 54 1
47 55 1
48 50 1
48 53 1
50 54 1
50 55 1
51 53 1
52 53 1
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 3 5
2 1 4 5
2 1 5 5
3 1 4 5
3 1 5 5
4 1 5 5
1 5 6 5
1 5 7 5
1 5 11 5
6 5 7 5
6 5 11 5
7 5 11 5
5 7 8 5
5 7 9 5
5 7 10 5
8 7 9 5
8 7 10 5
9 7 10 5
5 11 12 5
5 11 13 5
12 11 13 5
11 13 14 5
11 13 17 5
14 13 17 5
13 14 15 5
13 14 16 5
13 14 22 5
15 14 16 5
15 14 22 5
16 14 22 5
13 17 18 5
13 17 19 5
13 17 25 5
18 17 19 5
18 17 25 5
19 17 25 5
17 19 20 5
17 19 21 5
17 19 22 5
20 19 21 5
20 19 22 5
21 19 22 5
14 22 19 5
14 22 23 5
14 22 24 5
19 22 23 5
19 22 24 5
23 22 24 5
17 25 26 5
17 25 27 5
26 25 27 5
25 27 28 5
25 27 29 5
28 27 29 5
27 29 30 5
27 29 31 5
27 29 32 5
30 29 31 5
30 29 32 5
31 29 32 5
29 32 33 5
29 32 34 5
33 32 34 5
32 34 35 5
32 34 36 5
35 34 36 5
34 36 37 5
34 36 38 5
34 36 56 5
37 36 38 5
37 36 56 5
38 36 56 5
36 38 39 5
36 38 40 5
36 38 41 5
39 38 40 5
39 38 41 5
40 38 41 5
38 41 42 5
38 41 43 5
38 41 44 5
42 41 43 5
42 41 44 5
43 41 44 5
41 44 45 5
41 44 46 5
41 44 47 5
45 44 46 5
45 44 47 5
46 44 47 5
44 47 48 5
44 47 49 5
48 47 49 5
47 49 50 5
47 49 53 5
50 49 53 5
49 50 51 5
49 50 52 5
51 50 52 5
49 53 54 5
49 53 55 5
54 53 55 5
36 56 57 5
36 56 58 5
57 56 58 5
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
2 1 5 6 9
2 1 5 7 9
2 1 5 11 9
3 1 5 6 9
3 1 5 7 9
3 1 5 11 9
4 1 5 6 9
4 1 5 7 9
4 1 5 11 9
1 5 7 8 9
1 5 7 9 9
1 5 7 10 9
6 5 7 8 9
6 5 7 9 9
6 5 7 10 9
11 5 7 8 9
11 5 7 9 9
11 5 7 10 9
1 5 11 12 9
1 5 11 13 9
6 5 11 12 9
6 5 11 13 9
7 5 11 12 9
7 5 11 13 9
5 11 13 14 9
5 11 13 17 9
12 11 13 14 9
12 11 13 17 9
11 13 14 15 9
11 13 14 16 9
11 13 14 22 9
17 13 14 15 9
17 13 14 16 9
17 13 14 22 9
11 13 17 18 9
11 13 17 19 9
11 13 17 25 9
14 13 17 18 9
14 13 17 19 9
14 13 17 25 9
13 14 22 19 9
13 14 22 23 9
13 14 22 24 9
15 14 22 19 9
15 14 22 23 9
15 14 22 24 9
16 14 22 19 9
16 14 22 23 9
16 14 22 24 9
13 17 19 20 9
13 17 19 21 9
13 17 19 22 9
18 17 19 20 9
18 17 19 21 9
18 17 19 22 9
25 17 19 20 9
25 17 19 21 9
25 17 19 22 9
13 17 25 26 9
13 17 25 27 9
18 17 25 26 9
18 17 25 27 9
19 17 25 26 9
19 17 25 27 9
17 19 22 14 9
17 19 22 23 9
17 19 22 24 9
20 19 22 14 9
20 19 22 23 9
20 19 22 24 9
21 19 22 14 9
21 19 22 23 9
21 19 22 24 9
17 25 27 28 9
17 25 27 29 9
26 25 27 28 9
26 25 27 29 9
25 27 29 30 9
25 27 29 31 9
25 27 29 32 9
28 27 29 30 9
28 27 29 31 9
28 27 29 32 9
27 29 32 33 9
27 29 32 34 9
30 29 32 33 9
30 29 32 34 9
31 29 32 33 9
31 29 32 34 9
29 32 34 35 9
29 32 34 36 9
33 32 34 35 9
33 32 34 36 9
32 34 36 37 9
32 34 36 38 9
32 34 36 56 9
35 34 36 37 9
35 34 36 38 9
35 34 36 56 9
34 36 38 39 9
34 36 38 40 9
34 36 38 41 9
37 36 38 39 9
37 36 38 40 9
37 36 38 41 9
56 36 38 39 9
56 36 38 40 9
56 36 38 41 9
34 36 56 57 9
34 36 56 58 9
37 36 56 57 9
37 36 56 58 9
38 36 56 57 9
38 36 56 58 9
36 38 41 42 9
36 38 41 43 9
36 38 41 44 9
39 38 41 42 9
39 38 41 43 9
39 38 41 44 9
40 38 41 42 9
40 38 41 43 9
40 38 41 44 9
38 41 44 45 9
38 41 44 46 9
38 41 44 47 9
42 41 44 45 9
42 41 44 46 9
42 41 44 47 9
43 41 44 45 9
43 41 44 46 9
43 41 44 47 9
41 44 47 48 9
41 44 47 49 9
45 44 47 48 9
45 44 47 49 9
46 44 47 48 9
46 44 47 49 9
44 47 49 50 9
44 47 49 53 9
48 47 49 50 9
48 47 49 53 9
47 49 50 51 9
47 49 50 52 9
53 49 50 51 9
53 49 50 52 9
47 49 53 54 9
47 49 53 55 9
50 49 53 54 9
50 49 53 55 9
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3
11 5 13 12 2
13 11 17 14 2
25 17 27 26 2
27 25 29 28 2
32 29 34 33 2
34 32 36 35 2
47 53 50 49 2
49 52 51 50 2
49 55 54 53 2
56 36 58 57 2
[ system ]
; Name
Protein
[ molecules ]
; Compound #mols
Protein 1
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