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gaff2.py
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gaff2.py
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from textwrap import dedent
# AMBER General Force Field for organic molecules (Version 2.11, May 2016)
gaff_atom_types = dedent("""
c 12.01 0.616 Sp2 C carbonyl group
cs 12.01 0.616 Sp2 C in c=S
c1 12.01 0.360 Sp C
c2 12.01 0.360 Sp2 C
c3 12.01 0.878 Sp3 C
ca 12.01 0.360 Sp2 C in pure aromatic systems
cp 12.01 0.360 Head Sp2 C that connect two rings in biphenyl sys.
cq 12.01 0.360 Head Sp2 C that connect two rings in biphenyl sys. identical to cp
cc 12.01 0.360 Sp2 carbons in non-pure aromatic systems
cd 12.01 0.360 Sp2 carbons in non-pure aromatic systems, identical to cc
ce 12.01 0.360 Inner Sp2 carbons in conjugated systems
cf 12.01 0.360 Inner Sp2 carbons in conjugated systems, identical to ce
cg 12.01 0.360 Inner Sp carbons in conjugated systems
ch 12.01 0.360 Inner Sp carbons in conjugated systems, identical to cg
cx 12.01 0.360 Sp3 carbons in triangle systems
cy 12.01 0.360 Sp3 carbons in square systems
cu 12.01 0.360 Sp2 carbons in triangle systems
cv 12.01 0.360 Sp2 carbons in square systems
cz 12.01 0.360 Sp2 carbon in guanidine group
h1 1.008 0.135 H bonded to aliphatic carbon with 1 electrwd. group
h2 1.008 0.135 H bonded to aliphatic carbon with 2 electrwd. group
h3 1.008 0.135 H bonded to aliphatic carbon with 3 electrwd. group
h4 1.008 0.135 H bonded to non-sp3 carbon with 1 electrwd. group
h5 1.008 0.135 H bonded to non-sp3 carbon with 2 electrwd. group
ha 1.008 0.135 H bonded to aromatic carbon
hc 1.008 0.135 H bonded to aliphatic carbon without electrwd. group
hn 1.008 0.161 H bonded to nitrogen atoms
ho 1.008 0.135 Hydroxyl group
hp 1.008 0.135 H bonded to phosphate
hs 1.008 0.135 Hydrogen bonded to sulphur
hw 1.008 0.135 Hydrogen in water
hx 1.008 0.135 H bonded to C next to positively charged group
f 19.00 0.320 Fluorine
cl 35.45 1.910 Chlorine
br 79.90 2.880 Bromine
i 126.9 4.690 Iodine
n 14.01 0.530 Sp2 nitrogen in amide groups
n1 14.01 0.530 Sp N
n2 14.01 0.530 aliphatic Sp2 N with two connected atoms
n3 14.01 0.530 Sp3 N with three connected atoms
n4 14.01 0.530 Sp3 N with four connected atoms
na 14.01 0.530 Sp2 N with three connected atoms
nb 14.01 0.530 Sp2 N in pure aromatic systems
nc 14.01 0.530 Sp2 N in non-pure aromatic systems
nd 14.01 0.530 Sp2 N in non-pure aromatic systems, identical to nc
ne 14.01 0.530 Inner Sp2 N in conjugated systems
nf 14.01 0.530 Inner Sp2 N in conjugated systems, identical to ne
nh 14.01 0.530 Amine N connected one or more aromatic rings
no 14.01 0.530 Nitro N
ns 14.01 0.530 amind N, with 1 attached hydrogen atom
nt 14.01 0.530 amide N, with 2 attached hydrogen atoms
nx 14.01 0.530 like n4, but only has one hydrogen atom
ny 14.01 0.530 like n4, but only has two hydrogen atoms
nz 14.01 0.530 like n4, but only has three three hydrogen atoms
n+ 14.01 0.530 NH4+
nu 14.01 0.530 like nh, but only has one attached hydrogen atom
nv 14.01 0.530 like nh, but only has two attached hydrogen atoms
n7 14.01 0.530 like n3, but only has one attached hydrogen atom
n8 14.01 0.530 like n3, but only has two attached hydrogen atoms
n9 14.01 0.530 NH3
ni 14.01 0.530 like n in RG3
nj 14.01 0.530 like n in RG4
nk 14.01 0.530 like n4/nx/ny in RG3
nl 14.01 0.530 like n4/nx/ny in RG4
nm 14.01 0.530 like nh in RG3
nn 14.01 0.530 like nh in RG4
np 14.01 0.530 like n3 in RG3
nq 14.01 0.530 like n3 in RG4
n5 14.01 0.530 like n7 in RG3
n6 14.01 0.530 like n7 in RG4
o 16.00 0.434 Oxygen with one connected atom
oh 16.00 0.465 Oxygen in hydroxyl group
op 16.00 0.465
oq 16.00 0.465
os 16.00 0.465 Ether and ester oxygen
ow 16.00 0.465 Oxygen in water
p2 30.97 1.538 Phosphate with two connected atoms
p3 30.97 1.538 Phosphate with three connected atoms, such as PH3
p4 30.97 1.538 Phosphate with three connected atoms, such as O=P(CH3)2
p5 30.97 1.538 Phosphate with four connected atoms, such as O=P(OH)3
pb 30.97 1.538 Sp2 P in pure aromatic systems
pc 30.97 1.538 Sp2 P in non-pure aromatic systems
pd 30.97 1.538 Sp2 P in non-pure aromatic systems, identical to pc
pe 30.97 1.538 Inner Sp2 P in conjugated systems
pf 30.97 1.538 Inner Sp2 P in conjugated systems, identical to pe
px 30.97 1.538 Special p4 in conjugated systems
py 30.97 1.538 Special p5 in conjugated systems
s 32.06 2.900 S with one connected atom
s2 32.06 2.900 S with two connected atom, involved at least one double bond
s4 32.06 2.900 S with three connected atoms
s6 32.06 2.900 S with four connected atoms
sh 32.06 2.900 Sp3 S connected with hydrogen
sp 32.06 2.900
sq 32.06 2.900
ss 32.06 2.900 Sp3 S in thio-ester and thio-ether
sx 32.06 2.900 Special s4 in conjugated systems
sy 32.06 2.900 Special s6 in conjugated systems
""")
# hn ho hs n na nc nd ne nf n2 n3 n4 o oh os ow sh ss
gaff_bonds = dedent("""
ow-hw 553.0 0.9572 TIP3P_Water 1
hw-hw 553.0 1.5136 TIP3P_Water 1
br-br 81.0 2.5420 SOURCE1 4
br-c1 227.0 1.7870 SOURCE2 4 0.0024
br-c2 168.9 1.8930 SOURCE1_SOURCE5 25 0.0078
br-c 146.5 1.9460 SOURCE2 2 0.0285
br-c3 134.7 1.9780 SOURCE1_SOURCE5 146 0.0118
br-ca 162.2 1.9080 SOURCE1_SOURCE5 462 0.0052
br-cc 172.5 1.8850 SOURCE4_SOURCE5 128 0.0078
br-cx 150.0 1.9370 5/2017 11 0.0019
br-n1 141.5 1.8600 SOUECE3 1
br-n2 88.5 2.0380 SOURCE3 5 0.1082
br-n 136.5 1.8730 SOURCE3 4 0.0046
br-n3 110.4 1.9520 SOURCE3 2
br-n4 118.3 1.9260 SOURCE3 3 0.0013
br-na 97.0 2.0020 SOURCE3 7 0.2156
br-nh 112.8 1.9440 SOURCE3 1
br-no 75.7 2.1010 SOURCE3 1
br-o 193.6 1.8000 SOUECE3 1
br-oh 160.9 1.8660 SOURCE3 1
br-os 151.9 1.8870 SOURCE3 2
br-p2 133.1 2.2100 SOURCE3 9 0.0510
br-p3 126.8 2.2310 SOURCE3 3 0.0101
br-p4 145.9 2.1710 SOUECE3 1
br-p5 137.5 2.1960 SOURCE3 3 0.0099
br-s 169.2 2.2200 SOUECE3 1
br-s4 128.8 2.3410 SOURCE3 1
br-s6 171.6 2.2140 SOURCE3 3 0.0443
br-sh 173.6 2.2090 SOURCE3 1
br-ss 176.0 2.2030 SOURCE3 3 0.0035
c1-c1 837.3 1.1980 SOURCE1_SOURCE5 659 0.0039
c1-c2 535.9 1.3070 SOURCE1 18
c1-c3 295.9 1.4670 SOURCE1_SOURCE5 795 0.0034
c1-ca 325.6 1.4400 SOUECE3 1
c1-ce 518.7 1.3150 SOURCE4 6 0.0086
c1-cg 776.8 1.2160 SOURCE3_SOURCE5 179 0.0036
c1-ch 765.4 1.2190 SOURCE3_SOURCE5 13 0.0016
c1-cl 261.5 1.6310 SOURCE2 6 0.0050
c1-cx 319.9 1.4450 5/2017 24 0.0043
c1-f 482.2 1.2700 SOURCE2 2 0.0085
c1-ha 433.7 1.0670 SOURCE3_SOURCE5 343 0.0013
c1-hc 448.2 1.0600 SOUECE3 1
c1-i 153.5 1.9890 SOURCE2 4 0.0032
c1-n1 891.5 1.1530 SOURCE1_SOURCE5 481 0.0035
c1-n2 736.8 1.1970 SOURCE3_SOURCE5 36 0.0076
c1-n3 401.0 1.3470 SOURCE2_SOURCE5 10 0.0093
c1-n4 309.6 1.4170 SOURCE3 3 0.0032
c1-n 428.9 1.3300 SOUECE3 1
c1-na 379.5 1.3620 SOURCE3 8 0.0034
c1-ne 720.5 1.2020 SOURCE4_SOURCE5 31 0.0124
c1-nf 720.5 1.2020 SOURCE4_SOURCE5 21 0.0141
c1-nh 409.0 1.3420 SOURCE4_SOURCE5 33 0.0061
c1-no 323.5 1.4050 SOURCE3 3 0.0005
c1-o 795.0 1.1720 SOURCE2_SOURCE5 31 0.0068
c1-oh 422.2 1.3260 SOURCE3 1
c1-os 435.4 1.3180 SOURCE3_SOURCE5 8 0.0079
c1-p2 216.0 1.7700 SOUECE3 1
c1-p3 203.9 1.7900 SOUECE3 1
c1-p4 203.9 1.7900 SOUECE3 1
c1-p5 227.0 1.7530 SOURCE3 2
c1-s2 380.5 1.5950 SOURCE3 1
c1-s 370.6 1.6030 SOURCE1_SOURCE5 37 0.0043
c1-s4 239.0 1.7460 SOURCE3 2
c1-s6 256.6 1.7220 SOURCE3 2
c1-sh 291.4 1.6800 SOUECE3 1
c1-ss 282.8 1.6900 SOURCE1_SOURCE5 49 0.0113
c2-c2 481.8 1.3340 SOURCE1_SOURCE5 3727 0.0053
c2-c3 255.6 1.5100 SOURCE1_SOURCE5 10204 0.0042
c2-ca 398.4 1.3850 SOUECE3_SOURCE5 9 0.0149
c2-cc 438.0 1.3590 SOURCE1_SOURCE5 882 0.0181
c2-cd 438.0 1.3590 SOURCE1_SOURCE5 882 0.0181
c2-ce 460.5 1.3460 SOURCE3_SOURCE5 3239 0.0058
c2-cf 460.5 1.3460 SOURCE3_SOURCE5 3177 0.0057
c2-cl 192.7 1.7310 SOURCE1_SOURCE5 290 0.0098
c2-cu 501.4 1.3240 5/2017 11 0.0010
c2-cx 278.0 1.4850 5/2017 76 0.0060
c2-cy 254.3 1.5110 5/2017 21 0.0067
c2-f 368.1 1.3390 SOURCE1_SOURCE5 35 0.0085
c2-h4 394.2 1.0870 SOURCE3_SOURCE5 517 0.0028
c2-h5 386.1 1.0910 SOURCE4_SOURCE5 116 0.0021
c2-ha 392.2 1.0880 SOURCE3_SOURCE5 5991 0.0019
c2-hc 393.9 1.0870 SOURCE3 789 0.0046
c2-hx 401.4 1.0830 SOURCE3 3 0.0008
c2-i 98.1 2.1700 SOURCE3_SOURCE5 7 0.0194
c2-n1 470.9 1.3060 SOURCE3 4 0.0161
c2-n2 518.7 1.2820 SOURCE1_SOURCE5 1004 0.0051
c2-n3 412.7 1.3400 SOUECE3 1
c2-n 330.2 1.3990 SOURCE3_SOURCE5 174 0.0100
c2-n4 221.4 1.5120 SOURCE3_SOURCE5 21 0.0133
c2-na 327.7 1.4010 SOURCE3_SOURCE5 65 0.0179
c2-nc 458.2 1.3130 SOURCE1 99 0.0095
c2-nd 458.2 1.3130 SOURCE1 99
c2-ne 498.8 1.2920 SOURCE3_SOURCE5 310 0.0099
c2-nf 498.8 1.2920 SOURCE3_SOURCE5 273 0.0098
c2-nh 345.4 1.3870 SOURCE3_SOURCE5 1559 0.0120
c2-no 276.9 1.4480 SOURCE4_SOURCE5 27 0.0139
c2-o 635.2 1.2250 SOURCE4_SOURCE5 35 0.0033
c2-oh 402.3 1.3390 SOURCE1_SOURCE5 85 0.0126
c2-os 371.3 1.3600 SOURCE1_SOURCE5 548 0.0107
c2-p2 292.5 1.6690 SOURCE3_SOURCE5 87 0.0126
c2-p3 179.9 1.8340 SOURCE3 5 0.0042
c2-p4 186.1 1.8220 SOUECE3 1
c2-p5 166.2 1.8630 SOURCE4_SOURCE5 15 0.0083
c2-pe 275.1 1.6890 SOURCE3_SOURCE5 60 0.0472
c2-pf 275.1 1.6890 SOURCE3_SOURCE5 8 0.0019
c2-s2 362.6 1.6100 SOURCE2 1
c2-s 247.7 1.7340 SOURCE3 4 0.0034
c2-s4 229.4 1.7600 SOUECE3 1
c2-s6 229.4 1.7600 SOUECE3 1
c2-sh 215.2 1.7820 SOURCE4_SOURCE5 13 0.0077
c2-ss 246.2 1.7360 SOURCE1 209 0.0155
c3-c3 232.5 1.5380 SOURCE1_SOURCE5 88072 0.0058
c3-ca 250.3 1.5160 SOURCE1_SOURCE5 10699 0.0054
c3-cc 262.6 1.5020 SOURCE3_SOURCE5 3926 0.0049
c3-cd 262.6 1.5020 SOURCE3_SOURCE5 3926 0.0049
c3-ce 250.1 1.5160 SOURCE3_SOURCE5 1210 0.0060
c3-cf 250.2 1.5160 SOURCE3_SOURCE5 345 0.0071
c3-cl 155.5 1.8040 SOURCE1_SOURCE5 1173 0.0119
c3-cu 278.9 1.4840 5/2017 2
c3-cv 263.1 1.5010 5/2017 1
c3-cx 244.9 1.5220 5/2017 849 0.0062
c3-cy 235.3 1.5340 5/2017 522 0.0055
c3-f 352.6 1.3500 SOURCE1_SOURCE5 2188 0.0139
c3-h1 375.9 1.0970 SOURCE3_SOURCE5 112144 0.0055
c3-h2 377.3 1.0960 SOURCE3_SOURCE5 2681 0.0032
c3-h3 379.5 1.0950 SOURCE4_SOURCE5 64 0.0028
c3-hc 375.9 1.0970 SOURCE3_SOURCE5 133628 0.0015
c3-hx 386.5 1.0910 SOURCE3_SOURCE5 6495 0.0022
c3-i 89.0 2.2120 SOURCE1_SOURCE5 35 0.0128
c3-n1 292.3 1.4330 SOURCE3_SOURCE5 7 0.0033
c3-n2 259.9 1.4660 SOURCE1_SOURCE5 816 0.0087
c3-n 263.8 1.4620 SOURCE1_SOURCE5 4576 0.0061
c3-n3 261.2 1.4650 SOURCE1_SOURCE5 15206 0.0039
c3-n4 222.6 1.5110 SOURCE1_SOURCE5 2375 0.0125
c3-na 262.9 1.4630 SOURCE3_SOURCE5 1732 0.0077
c3-nc 269.3 1.4560 SOURCE3 9 0.0109
c3-nd 269.3 1.4560 SOURCE3 9
c3-nh 261.8 1.4640 SOURCE3_SOURCE5 3492 0.0064
c3-no 206.4 1.5330 SOURCE1_SOURCE5 150 0.0187
c3-o 438.1 1.3170 SOURCE4 8 0.0193
c3-oh 293.4 1.4230 SOURCE1_SOURCE5 8884 0.0067
c3-os 284.8 1.4320 SOURCE1_SOURCE5 17971 0.0103
c3-p2 169.7 1.8550 SOURCE3 9 0.0125
c3-p3 168.2 1.8580 SOURCE3_SOURCE5 221 0.0094
c3-p4 177.6 1.8390 SOURCE3_SOURCE5 45 0.0106
c3-p5 177.2 1.8390 SOURCE1_SOURCE5 408 0.0183
c3-px 182.7 1.8290 SOURCE3_SOURCE5 35 0.0083
c3-py 177.1 1.8400 SOURCE3_SOURCE5 39 0.0126
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nh-ss 291.5 1.7090 SOURCE1_SOURCE5 58 0.0020
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n -n 250.8 1.4040 SOURCE3_SOURCE5 47 0.0125
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no-o 367.9 1.2260 SOURCE1_SOURCE5 4403 0.0099
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no-os 172.2 1.4210 SOURCE4_SOURCE5 138 0.0070
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n -p5 238.9 1.7170 SOURCE4_SOURCE5 25 0.0133
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n -s 245.6 1.7670 SOURCE3 3 0.0011
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oh-os 129.1 1.4560 SOURCE4_SOURCE5 49 0.0046
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oh-p5 346.0 1.6150 SOURCE3_SOURCE5 1121 0.0129
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oh-sy 356.0 1.6500 SOURCE4_SOURCE5 123 0.0037
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p2-p5 110.4 2.1800 SOUECE3 1
p2-pe 244.9 1.8670 SOURCE3 16 0.3571
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p2-s 375.1 1.7720 SOURCE3 26 0.3014
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p2-sh 217.0 1.9710 SOURCE3 10 0.2829
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p3-p4 101.5 2.2160 SOURCE3 3 0.0011
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p3-s4 161.8 2.0870 SOURCE3 8 0.2235
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p3-ss 148.9 2.1210 SOURCE3 3 0.0059
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p4-s6 105.2 2.2690 SOUECE3 1
p4-sh 151.0 2.1150 SOURCE3 4 0.0008
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p5-s 239.2 1.9340 SOURCE1_SOURCE5 173 0.0138
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p5-s6 181.8 2.0400 SOUECE3 1
p5-sh 163.8 2.0820 SOURCE3 3 0.0035
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pe-px 169.8 2.0050 SOURCE3 12 0.2609
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cf-no 262.7 1.4630 SOURCE5 3 0.0129
cx-op 279.3 1.4370 5/2017 666 0.0065
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cx-np 256.4 1.4700 5/2017 185 0.0035
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np-p5 250.0 1.7020 5/2017 41 0.0041
cy-nq 245.9 1.4820 5/2017 52 0.0039
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op-op 80.1 1.5970 5/2017 2 0.0081
cy-p5 153.7 1.8910 5/2017 2
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