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added AMBER parameters for tutorial
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@stefdoerr
stefdoerr committed Jun 11, 2024
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130 changes: 130 additions & 0 deletions mor/MOL.cif
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data_MOL
#
#
_chem_comp.id MOL
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_formal_charge 1
##
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
MOL O1 os O 0 -0.3466175 -2.724 -0.151 -1.387 -2.724 -0.151 -1.387
MOL O2 oh O 0 -0.63509345 0.895 2.477 -0.799 0.895 2.477 -0.799
MOL O3 o O 0 -0.43236506 -3.873 2.064 -0.400 -3.873 2.064 -0.400
MOL O4 oh O 0 -0.55507207 -4.263 -2.289 -0.051 -4.263 -2.289 -0.051
MOL N1 nx N 1 0.008024579 2.198 0.273 -0.143 2.198 0.273 -0.143
MOL C1 c3 C 0 0.00786599 -0.605 0.612 -0.730 -0.605 0.612 -0.730
MOL C2 c3 C 0 0.057475276 0.181 1.642 0.094 0.181 1.642 0.094
MOL C3 c3 C 0 -0.059390176 1.239 0.832 0.896 1.239 0.832 0.896
MOL C4 c3 C 0 0.036433775 -1.958 1.043 -1.358 -1.958 1.043 -1.358
MOL C5 c3 C 0 -0.09467384 0.332 -0.020 -1.776 0.332 -0.020 -1.776
MOL C6 ca C 0 -0.026924675 -1.135 -0.447 0.197 -1.135 -0.447 0.197
MOL C7 c3 C 0 -0.19447857 -0.730 2.490 0.983 -0.730 2.490 0.983
MOL C8 c3 C 0 -0.16588403 1.542 -0.670 -1.114 1.542 -0.670 -1.114
MOL C9 c3 C 0 -0.05305423 0.685 -0.242 1.858 0.685 -0.242 1.858
MOL C10 ca C 0 0.03806969 -0.570 -0.923 1.350 -0.570 -0.923 1.350
MOL C11 c3 C 0 -0.22416082 3.474 -0.285 0.434 3.474 -0.285 0.434
MOL C12 c3 C 0 0.00397262 -1.833 3.154 0.143 -1.833 3.154 0.143
MOL C13 cx C 0 -0.09396583 4.606 -0.220 -0.557 4.606 -0.220 -0.557
MOL C14 c C 0 0.44287938 -2.695 2.099 -0.520 -2.695 2.099 -0.520
MOL C15 ca C 0 0.09308282 -2.350 -0.863 -0.284 -2.350 -0.863 -0.284
MOL C16 cx C 0 -0.22249568 5.290 1.095 -0.830 5.290 1.095 -0.830
MOL C17 cx C 0 -0.22249568 5.994 0.037 -0.051 5.994 0.037 -0.051
MOL C18 ca C 0 -0.25761002 -1.277 -1.929 2.011 -1.277 -1.929 2.011
MOL C19 ca C 0 0.3065762 -3.069 -1.845 0.360 -3.069 -1.845 0.360
MOL C20 ca C 0 -0.27642775 -2.488 -2.383 1.512 -2.488 -2.383 1.512
MOL H1 hx H 0 0.13226037 1.845 1.530 1.461 1.845 1.530 1.461
MOL H2 h1 H 0 0.15269378 -1.863 1.404 -2.374 -1.863 1.404 -2.374
MOL H3 hc H 0 0.10215452 -0.198 -0.790 -2.324 -0.198 -0.790 -2.324
MOL H4 hc H 0 0.10215452 0.652 0.728 -2.490 0.652 0.728 -2.490
MOL H5 hc H 0 0.1239905 -1.181 1.881 1.755 -1.181 1.881 1.755
MOL H6 hc H 0 0.1239905 -0.137 3.249 1.490 -0.137 3.249 1.490
MOL H7 hx H 0 0.13954657 1.267 -1.553 -0.559 1.267 -1.553 -0.559
MOL H8 hx H 0 0.13954657 2.286 -0.940 -1.847 2.286 -0.940 -1.847
MOL H9 hc H 0 0.067569 0.463 0.266 2.792 0.463 0.266 2.792
MOL H10 hc H 0 0.067569 1.462 -0.958 2.104 1.462 -0.958 2.104
MOL H11 hx H 0 0.17592822 3.704 0.305 1.310 3.704 0.305 1.310
MOL H12 hx H 0 0.17592822 3.274 -1.299 0.748 3.274 -1.299 0.748
MOL H13 hc H 0 0.040343422 -1.397 3.789 -0.624 -1.397 3.789 -0.624
MOL H14 hc H 0 0.040343422 -2.474 3.768 0.760 -2.474 3.768 0.760
MOL H15 hc H 0 0.13437337 4.533 -0.905 -1.383 4.533 -0.905 -1.383
MOL H16 hc H 0 0.13343094 4.957 1.969 -0.295 4.957 1.969 -0.295
MOL H17 hc H 0 0.13343094 5.611 1.294 -1.836 5.611 1.294 -1.836
MOL H18 hc H 0 0.13343094 6.797 -0.499 -0.522 6.797 -0.499 -0.522
MOL H19 hc H 0 0.13343094 6.131 0.193 1.004 6.131 0.193 1.004
MOL H20 ho H 0 0.4475763 1.009 3.347 -0.438 1.009 3.347 -0.438
MOL H21 ha H 0 0.19207886 -0.903 -2.351 2.927 -0.903 -2.351 2.927
MOL H22 ha H 0 0.23492707 -3.034 -3.147 2.033 -3.034 -3.147 2.033
MOL H23 ho H 0 0.44779718 -4.610 -1.740 -0.745 -4.610 -1.740 -0.745
MOL H24 hn H 0 0.2918338 2.463 1.086 -0.681 2.463 1.086 -0.681
##
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
MOL O1 C4 SING
MOL O1 C15 SING
MOL O2 C2 SING
MOL O2 H20 SING
MOL O3 C14 DOUB
MOL O4 C19 SING
MOL O4 H23 SING
MOL N1 C3 SING
MOL N1 C8 SING
MOL N1 C11 SING
MOL N1 H24 SING
MOL C1 C2 SING
MOL C1 C4 SING
MOL C1 C5 SING
MOL C1 C6 SING
MOL C2 C3 SING
MOL C2 C7 SING
MOL C3 C9 SING
MOL C3 H1 SING
MOL C4 C14 SING
MOL C4 H2 SING
MOL C5 C8 SING
MOL C5 H3 SING
MOL C5 H4 SING
MOL C6 C10 DOUB
MOL C6 C15 SING
MOL C7 C12 SING
MOL C7 H5 SING
MOL C7 H6 SING
MOL C8 H7 SING
MOL C8 H8 SING
MOL C9 C10 SING
MOL C9 H9 SING
MOL C9 H10 SING
MOL C10 C18 SING
MOL C11 C13 SING
MOL C11 H11 SING
MOL C11 H12 SING
MOL C12 C14 SING
MOL C12 H13 SING
MOL C12 H14 SING
MOL C13 C16 SING
MOL C13 C17 SING
MOL C13 H15 SING
MOL C15 C19 DOUB
MOL C16 C17 SING
MOL C16 H16 SING
MOL C16 H17 SING
MOL C17 H18 SING
MOL C17 H19 SING
MOL C18 C20 DOUB
MOL C18 H21 SING
MOL C19 C20 SING
MOL C20 H22 SING
##
177 changes: 177 additions & 0 deletions mor/MOL.frcmod
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Frcmod generated by HTMD parameterize version 2.8.11
MASS
c 12.010 0.00
c3 12.010 0.00
ca 12.010 0.00
cx 12.010 0.00
h1 1.008 0.00
ha 1.008 0.00
hc 1.008 0.00
hn 1.008 0.00
ho 1.008 0.00
hx 1.008 0.00
nx 14.010 0.00
o 16.000 0.00
oh 16.000 0.00
os 16.000 0.00

BOND
c -c3 243.200 1.524
c -o 652.600 1.218
c3-c3 232.500 1.538
c3-ca 250.300 1.516
c3-cx 244.900 1.522
c3-h1 375.900 1.097
c3-hc 375.900 1.097
c3-hx 386.500 1.091
c3-nx 222.600 1.511
c3-oh 293.400 1.423
c3-os 284.800 1.432
ca-ca 378.600 1.398
ca-ha 395.700 1.086
ca-oh 365.600 1.364
ca-os 357.500 1.370
cx-cx 256.900 1.508
cx-hc 393.900 1.087
hn-nx 482.900 1.030
ho-oh 563.500 0.973

ANGL
c -c3-c3 65.300 111.040
c -c3-h1 47.500 108.220
c -c3-hc 47.400 108.770
c -c3-os 85.300 109.210
c3-c -c3 64.000 116.500
c3-c -o 84.600 123.200
c3-c3-c3 64.900 111.510
c3-c3-ca 65.200 112.070
c3-c3-h1 46.900 109.560
c3-c3-hc 46.800 109.800
c3-c3-hx 46.700 110.560
c3-c3-nx 81.000 114.210
c3-c3-oh 84.600 110.190
c3-c3-os 85.300 107.970
c3-ca-ca 65.600 120.770
c3-cx-cx 63.400 120.110
c3-cx-hc 46.300 114.480
c3-nx-c3 64.500 109.660
c3-nx-hn 46.200 110.110
c3-oh-ho 49.000 107.260
c3-os-ca 66.100 117.960
ca-c3-hc 47.300 110.470
ca-ca-ca 68.800 120.020
ca-ca-ha 48.700 119.880
ca-ca-oh 87.200 119.900
ca-ca-os 87.300 119.200
ca-oh-ho 50.700 108.580
cx-c3-hx 46.700 112.700
cx-c3-nx 86.400 101.420
cx-cx-cx 90.200 60.000
cx-cx-hc 46.100 117.690
h1-c3-os 62.400 109.780
hc-c3-hc 39.000 107.580
hc-cx-hc 38.100 114.430
hx-c3-hx 38.800 109.750
hx-c3-nx 60.100 108.010

DIHE
c -c3-c3-c3 1 0.10000000 0.000 3.0 SCEE=1.2 SCNB=2.0
c -c3-c3-ca 1 0.10000000 0.000 3.0 SCEE=1.2 SCNB=2.0
c -c3-c3-hc 1 0.15555556 0.000 3.0 SCEE=1.2 SCNB=2.0
c -c3-os-ca 1 0.38333333 0.000 3.0 SCEE=1.2 SCNB=2.0
c3-c -c3-c3 1 0.33200000 180.000 2.0 SCEE=1.2 SCNB=2.0
c3-c -c3-h1 1 0.00000000 180.000 2.0 SCEE=1.2 SCNB=2.0
c3-c -c3-hc 1 0.00000000 0.000 2.0 SCEE=1.2 SCNB=2.0
c3-c -c3-os 1 0.00000000 180.000 2.0 SCEE=1.2 SCNB=2.0
c3-c3-c -c3 1 0.33200000 180.000 2.0 SCEE=1.2 SCNB=2.0
c3-c3-c -o 1 0.03000000 180.000 -2.0 SCEE=1.2 SCNB=2.0
c3-c3-c -o 1 0.55000000 180.000 -3.0 SCEE=1.2 SCNB=2.0
c3-c3-c -o 1 0.74000000 0.000 1.0 SCEE=1.2 SCNB=2.0
c3-c3-c3-c3 1 0.13000000 0.000 -3.0 SCEE=1.2 SCNB=2.0
c3-c3-c3-c3 1 0.29000000 180.000 -2.0 SCEE=1.2 SCNB=2.0
c3-c3-c3-c3 1 0.11000000 0.000 1.0 SCEE=1.2 SCNB=2.0
c3-c3-c3-ca 1 0.15555556 0.000 3.0 SCEE=1.2 SCNB=2.0
c3-c3-c3-h1 1 0.15555556 0.000 3.0 SCEE=1.2 SCNB=2.0
c3-c3-c3-hc 1 0.08000000 0.000 3.0 SCEE=1.2 SCNB=2.0
c3-c3-c3-hx 1 0.15555556 0.000 3.0 SCEE=1.2 SCNB=2.0
c3-c3-c3-nx 1 0.21000000 0.000 3.0 SCEE=1.2 SCNB=2.0
c3-c3-c3-oh 1 0.21000000 0.000 3.0 SCEE=1.2 SCNB=2.0
c3-c3-c3-os 1 0.15555556 0.000 3.0 SCEE=1.2 SCNB=2.0
c3-c3-ca-ca 1 0.24500000 180.000 2.0 SCEE=1.2 SCNB=2.0
c3-c3-nx-c3 1 0.15600000 0.000 3.0 SCEE=1.2 SCNB=2.0
c3-c3-nx-hn 1 0.15555556 0.000 3.0 SCEE=1.2 SCNB=2.0
c3-c3-oh-ho 1 0.00000000 0.000 3.0 SCEE=1.2 SCNB=2.0
c3-c3-os-ca 1 0.38333333 0.000 3.0 SCEE=1.2 SCNB=2.0
c3-ca-ca-c3 1 3.62500000 180.000 2.0 SCEE=1.2 SCNB=2.0
c3-ca-ca-ca 1 3.62500000 180.000 2.0 SCEE=1.2 SCNB=2.0
c3-ca-ca-ha 1 3.62500000 180.000 2.0 SCEE=1.2 SCNB=2.0
c3-ca-ca-os 1 3.62500000 180.000 2.0 SCEE=1.2 SCNB=2.0
c3-cx-cx-cx 1 0.15555556 0.000 3.0 SCEE=1.2 SCNB=2.0
c3-cx-cx-hc 1 0.15555556 0.000 3.0 SCEE=1.2 SCNB=2.0
c3-nx-c3-c3 1 0.15600000 0.000 3.0 SCEE=1.2 SCNB=2.0
c3-nx-c3-cx 1 0.15555556 0.000 3.0 SCEE=1.2 SCNB=2.0
c3-nx-c3-hx 1 0.15555556 0.000 3.0 SCEE=1.2 SCNB=2.0
c3-os-ca-ca 1 1.61000000 180.000 2.0 SCEE=1.2 SCNB=2.0
ca-c3-c3-h1 1 0.15555556 0.000 3.0 SCEE=1.2 SCNB=2.0
ca-c3-c3-hc 1 0.15555556 0.000 3.0 SCEE=1.2 SCNB=2.0
ca-c3-c3-hx 1 0.15555556 0.000 3.0 SCEE=1.2 SCNB=2.0
ca-c3-c3-nx 1 0.15555556 0.000 3.0 SCEE=1.2 SCNB=2.0
ca-c3-c3-oh 1 0.15555556 0.000 3.0 SCEE=1.2 SCNB=2.0
ca-c3-c3-os 1 0.15555556 0.000 3.0 SCEE=1.2 SCNB=2.0
ca-ca-c3-hc 1 0.00000000 180.000 2.0 SCEE=1.2 SCNB=2.0
ca-ca-ca-ca 1 3.62500000 180.000 2.0 SCEE=1.2 SCNB=2.0
ca-ca-ca-ha 1 3.62500000 180.000 2.0 SCEE=1.2 SCNB=2.0
ca-ca-ca-oh 1 3.62500000 180.000 2.0 SCEE=1.2 SCNB=2.0
ca-ca-ca-os 1 3.62500000 180.000 2.0 SCEE=1.2 SCNB=2.0
ca-ca-oh-ho 1 0.83500000 180.000 2.0 SCEE=1.2 SCNB=2.0
ca-os-c3-h1 1 0.38333333 0.000 3.0 SCEE=1.2 SCNB=2.0
cx-c3-nx-hn 1 0.15555556 0.000 3.0 SCEE=1.2 SCNB=2.0
cx-cx-c3-hx 1 0.08000000 0.000 3.0 SCEE=1.2 SCNB=2.0
cx-cx-c3-nx 1 0.21000000 0.000 3.0 SCEE=1.2 SCNB=2.0
cx-cx-cx-hc 1 0.15555556 0.000 3.0 SCEE=1.2 SCNB=2.0
h1-c3-c -o 1 0.80000000 0.000 -1.0 SCEE=1.2 SCNB=2.0
h1-c3-c -o 1 0.08000000 180.000 3.0 SCEE=1.2 SCNB=2.0
ha-ca-ca-ha 1 3.62500000 180.000 2.0 SCEE=1.2 SCNB=2.0
ha-ca-ca-oh 1 3.62500000 180.000 2.0 SCEE=1.2 SCNB=2.0
hc-c3-c -o 1 0.83000000 0.000 -1.0 SCEE=1.2 SCNB=2.0
hc-c3-c -o 1 0.04000000 180.000 3.0 SCEE=1.2 SCNB=2.0
hc-c3-c3-hc 1 0.12000000 0.000 3.0 SCEE=1.2 SCNB=2.0
hc-c3-c3-hx 1 0.15555556 0.000 3.0 SCEE=1.2 SCNB=2.0
hc-c3-c3-nx 1 0.15555556 0.000 3.0 SCEE=1.2 SCNB=2.0
hc-c3-c3-oh 1 0.18000000 0.000 -3.0 SCEE=1.2 SCNB=2.0
hc-c3-c3-oh 1 0.51000000 0.000 1.0 SCEE=1.2 SCNB=2.0
hc-cx-c3-hx 1 0.12000000 0.000 3.0 SCEE=1.2 SCNB=2.0
hc-cx-c3-nx 1 0.15555556 0.000 3.0 SCEE=1.2 SCNB=2.0
hc-cx-cx-hc 1 0.15555556 0.000 3.0 SCEE=1.2 SCNB=2.0
hn-nx-c3-hx 1 0.10900000 0.000 3.0 SCEE=1.2 SCNB=2.0
hx-c3-c3-oh 1 0.15555556 0.000 3.0 SCEE=1.2 SCNB=2.0
nx-c3-c3-oh 1 0.14400000 0.000 -3.0 SCEE=1.2 SCNB=2.0
nx-c3-c3-oh 1 1.30000000 0.000 2.0 SCEE=1.2 SCNB=2.0
o -c -c3-os 1 0.63000000 180.000 -2.0 SCEE=1.2 SCNB=2.0
o -c -c3-os 1 1.00000000 180.000 -3.0 SCEE=1.2 SCNB=2.0
o -c -c3-os 1 0.08000000 0.000 1.0 SCEE=1.2 SCNB=2.0
oh-ca-ca-os 1 3.62500000 180.000 2.0 SCEE=1.2 SCNB=2.0

IMPR
o -c3-c -c3 10.50000000 180.000 2.0
c3-ca-ca-ca 1.10000000 180.000 2.0
ca-ca-ca-ha 1.10000000 180.000 2.0
oh-ca-ca-ca 1.10000000 180.000 2.0
os-ca-ca-ca 1.10000000 180.000 2.0

NONB
c 1.86060000 0.09880000
c3 1.90690000 0.10780000
ca 1.86060000 0.09880000
cx 1.90690000 0.10780000
h1 1.35930000 0.02080000
ha 1.47350000 0.01610000
hc 1.45930000 0.02080000
hn 0.62100000 0.01000000
ho 0.30190000 0.00470000
hx 1.05930000 0.02080000
nx 1.45280000 2.54530000
o 1.71070000 0.14630000
oh 1.82000000 0.09300000
os 1.77130000 0.07260000

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