diff --git a/src/data/amber_q/ABE.frg b/src/data/amber_q/ABE.frg new file mode 100644 index 0000000000..630684260d --- /dev/null +++ b/src/data/amber_q/ABE.frg @@ -0,0 +1,44 @@ +# This is an automatically generated segment file +# +$ABE + 20 + 1 C1 AC 3 0 1 1 -0.252626 0.000000 + 2 H1 H2 0 0 1 1 0.216755 0.000000 + 3 C2 CT 0 0 1 1 0.277475 0.000000 + 4 H2 H1 0 0 1 1 0.092812 0.000000 + 5 O2 OH 0 0 1 1 -0.608823 0.000000 + 6 HO2 HO 0 0 1 1 0.364969 0.000000 + 7 C3 CT 0 0 1 1 -0.146592 0.000000 + 82H3 HC 0 0 1 1 0.073592 0.000000 + 93H3 HC 0 0 1 1 0.073592 0.000000 + 10 C4 CT 0 0 1 1 0.153661 0.000000 + 11 H4 H1 0 0 1 1 0.042781 0.000000 + 12 O4 OH 0 0 1 1 -0.550610 0.000000 + 13 HO4 HO 0 0 1 1 0.362947 0.000000 + 14 C5 CT 0 0 1 1 0.114707 0.000000 + 15 H5 H1 0 0 1 1 0.062819 0.000000 + 16 OR OS 0 0 1 1 -0.276948 0.000000 + 17 C6 CT 0 0 1 1 -0.225880 0.000000 + 182H6 HC 0 0 1 1 0.075123 0.000000 + 193H6 HC 0 0 1 1 0.075123 0.000000 + 204H6 HC 0 0 1 1 0.075123 0.000000 + 1 2 + 1 3 + 1 16 + 3 4 + 3 5 + 3 7 + 5 6 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 + 10 14 + 12 13 + 14 15 + 14 16 + 14 17 + 17 18 + 17 19 + 17 20 diff --git a/src/data/amber_q/BTH.frg b/src/data/amber_q/BTH.frg new file mode 100644 index 0000000000..d367383d5c --- /dev/null +++ b/src/data/amber_q/BTH.frg @@ -0,0 +1,27 @@ +# This is an automatically generated segment file +# +$BTH + 12 + 1 C1 CT 3 0 1 1 -0.021034 0.000000 + 22H1 HC 0 0 1 1 0.010517 0.000000 + 33H1 HC 0 0 1 1 0.010517 0.000000 + 4 C2 CT 0 0 1 1 -0.012697 0.000000 + 52H2 HC 0 0 1 1 0.006349 0.000000 + 63H2 HC 0 0 1 1 0.006349 0.000000 + 7 C3 CT 0 0 1 1 -0.024254 0.000000 + 82H3 HC 0 0 1 1 0.012127 0.000000 + 93H3 HC 0 0 1 1 0.012127 0.000000 + 10 C4 CT 4 0 1 1 -0.010029 0.000000 + 112H4 HC 0 0 1 1 0.005014 0.000000 + 123H4 HC 0 0 1 1 0.005014 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 4 6 + 4 7 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 diff --git a/src/data/amber_q/BTO.frg b/src/data/amber_q/BTO.frg new file mode 100644 index 0000000000..0a3dd39a8e --- /dev/null +++ b/src/data/amber_q/BTO.frg @@ -0,0 +1,25 @@ +# This is an automatically generated segment file +# +$BTO + 11 + 1 C1 C 3 1 1 1 0.190650 0.000000 + 2 O1 O2 0 0 1 1 -0.340348 0.000000 + 3 C2 CT 0 0 1 1 -0.043202 0.000000 + 42H2 HC 0 0 1 1 0.059487 0.000000 + 53H2 HC 0 0 1 1 0.059487 0.000000 + 6 C3 CT 0 0 1 1 0.014628 0.000000 + 72H3 HC 0 0 1 1 0.039814 0.000000 + 83H3 HC 0 0 1 1 0.039814 0.000000 + 9 C4 CT 4 0 1 1 -0.003054 0.000000 + 102H4 HC 0 0 1 1 -0.008638 0.000000 + 113H4 HC 0 0 1 1 -0.008638 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 6 + 6 7 + 6 8 + 6 9 + 9 10 + 9 11 diff --git a/src/data/amber_q/BUT.frg b/src/data/amber_q/BUT.frg new file mode 100644 index 0000000000..2e66c48c13 --- /dev/null +++ b/src/data/amber_q/BUT.frg @@ -0,0 +1,29 @@ +# This is an automatically generated segment file +# +$BUT + 13 + 1 C1 CT 3 0 1 1 -0.011176 0.000000 + 22H1 HC 0 0 1 1 0.005588 0.000000 + 33H1 HC 0 0 1 1 0.005588 0.000000 + 4 C2 CT 0 0 1 1 -0.023686 0.000000 + 52H2 HC 0 0 1 1 0.011843 0.000000 + 63H2 HC 0 0 1 1 0.011843 0.000000 + 7 C3 CT 0 0 1 1 -0.006136 0.000000 + 82H3 HC 0 0 1 1 0.003068 0.000000 + 93H3 HC 0 0 1 1 0.003068 0.000000 + 10 C4 CT 0 0 1 1 0.091023 0.000000 + 112H4 HC 0 0 1 1 -0.030341 0.000000 + 123H4 HC 0 0 1 1 -0.030341 0.000000 + 134H4 HC 0 0 1 1 -0.030341 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 4 6 + 4 7 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 + 10 13 diff --git a/src/data/amber_q/CA.frg b/src/data/amber_q/CA.frg new file mode 100644 index 0000000000..ced088a9ab --- /dev/null +++ b/src/data/amber_q/CA.frg @@ -0,0 +1,4 @@ +# Fragment definition for Calcium cation +$CA + 1 + 1CA Ca 0 0 1 1 2.000000 0.000000 diff --git a/src/data/amber_q/Ca.sgm b/src/data/amber_q/Ca.sgm new file mode 100644 index 0000000000..977a8080b0 --- /dev/null +++ b/src/data/amber_q/Ca.sgm @@ -0,0 +1,5 @@ +# This is an automatically generated segment file +# + 1 0 0 0 0 + 1Ca Ca Ca Ca 1 1 0 0 + 2.000000 0.000000 2.000000 0.000000 2.000000 0.000000 diff --git a/src/data/amber_q/DTT.frg b/src/data/amber_q/DTT.frg new file mode 100644 index 0000000000..c6ef2739a1 --- /dev/null +++ b/src/data/amber_q/DTT.frg @@ -0,0 +1,91 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$DTT + 42 + 1 N1 N* 0 6 1 1 -0.023900 0.000000 + 2 C2 C 0 6 1 1 0.567700 0.000000 + 3 N3 NA 0 6 1 1 -0.434000 0.000000 + 4 H3 H 0 0 1 1 0.342000 0.000000 + 5 C4 C 0 6 1 1 0.519400 0.000000 + 6 C5 CM 0 6 1 1 0.002500 0.000000 + 7 C5M CT 0 0 1 1 -0.226900 0.000000 + 82H5M HC 0 0 1 1 0.077000 0.000000 + 93H5M HC 0 0 1 1 0.077000 0.000000 + 104H5M HC 0 0 1 1 0.077000 0.000000 + 11 C6 CM 0 6 1 1 -0.220900 0.000000 + 122H6 H4 0 0 1 1 0.260700 0.000000 + 13 O2 O 0 0 1 1 -0.588100 0.000000 + 14 O4 O 0 0 1 1 -0.556300 0.000000 + 15 C1* CT 0 0 1 1 0.068000 0.000000 + 162H1* H2 0 0 1 1 0.180400 0.000000 + 17 C2* CT 0 0 1 1 -0.085400 0.000000 + 182H2* HC 0 0 1 1 0.071800 0.000000 + 193H2* HC 0 0 1 1 0.071800 0.000000 + 20 C3* CT 0 0 1 1 0.071300 0.000000 + 212H3* H1 0 0 1 1 0.098500 0.000000 + 22 O3* OH 0 0 1 1 -0.654900 0.000000 + 233H3* HO 0 0 1 1 0.439600 0.000000 + 24 C4* CT 0 0 1 1 0.162900 0.000000 + 252H4* H1 0 0 1 1 0.117600 0.000000 + 26 O4* OS 0 0 1 1 -0.369100 0.000000 + 27 C5* CT 0 0 1 1 -0.006900 0.000000 + 282H5* H1 0 0 1 1 0.075400 0.000000 + 293H5* H1 0 0 1 1 0.075400 0.000000 + 30 O5* OS 0 0 1 1 -0.495400 0.000000 + 31 PA P 0 0 1 1 1.145727 0.000000 + 32 O1A O2 0 0 1 1 -.721001 0.000000 + 33 O2A O2 0 0 1 1 -.721001 0.000000 + 34 O3A OS 0 0 1 1 -.390741 0.000000 + 35 PB P 0 0 1 1 1.240313 0.000000 + 36 O1B O2 0 0 1 1 -.765956 0.000000 + 37 O2B O2 0 0 1 1 -.765956 0.000000 + 38 O3B OS 0 0 1 1 -.769623 0.000000 + 39 PG P 0 0 1 1 1.164170 0.000000 + 40 O1G O2 0 0 1 1 -.907458 0.000000 + 41 O2G O2 0 0 1 1 -.907458 0.000000 + 42 O3G O2 0 0 1 1 -.907458 0.000000 + 1 2 + 1 11 + 1 15 + 2 3 + 2 13 + 3 4 + 3 5 + 5 6 + 5 14 + 6 7 + 6 11 + 7 8 + 7 9 + 7 10 + 11 12 + 15 16 + 15 17 + 15 26 + 17 18 + 17 19 + 17 20 + 20 21 + 20 22 + 20 24 + 22 23 + 24 25 + 24 26 + 24 27 + 27 28 + 27 29 + 27 30 + 30 31 + 31 32 + 31 33 + 31 34 + 34 35 + 35 36 + 35 37 + 35 38 + 38 39 + 39 40 + 39 41 + 39 42 diff --git a/src/data/amber_q/EAM.frg b/src/data/amber_q/EAM.frg new file mode 100644 index 0000000000..630050a454 --- /dev/null +++ b/src/data/amber_q/EAM.frg @@ -0,0 +1,23 @@ +# This is an automatically generated segment file +# +$EAM + 10 + 1 C1 CT 3 0 1 1 -0.064862 0.000000 + 22H1 H1 0 0 1 1 0.086747 0.000000 + 33H1 H1 0 0 1 1 0.086747 0.000000 + 4 C2 CT 0 0 1 1 0.188179 0.000000 + 52H2 HP 0 0 1 1 0.044255 0.000000 + 63H2 HP 0 0 1 1 0.044255 0.000000 + 7 N3 N3 0 0 1 1 -0.202182 0.000000 + 82H3 H 0 0 1 1 0.272287 0.000000 + 93H3 H 0 0 1 1 0.272287 0.000000 + 104H3 H 0 0 1 1 0.272287 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 4 6 + 4 7 + 7 8 + 7 9 + 7 10 diff --git a/src/data/amber_q/GA1.frg b/src/data/amber_q/GA1.frg new file mode 100644 index 0000000000..d5555d4a6f --- /dev/null +++ b/src/data/amber_q/GA1.frg @@ -0,0 +1,48 @@ +# This is an automatically generated segment file +# +$GA1 + 22 + 1 C1 AC 3 0 1 1 -0.067884 0.000000 + 2 H1 H2 0 0 1 1 0.151312 0.000000 + 3 OR OS 0 0 1 1 -0.319184 0.000000 + 4 C2 CT 0 0 1 1 0.147069 0.000000 + 5 H2 H1 0 0 1 1 0.164883 0.000000 + 6 O2 OH 0 0 1 1 -0.636000 0.000000 + 7 HO2 HO 0 0 1 1 0.400609 0.000000 + 8 C3 CT 0 0 1 1 0.178265 0.000000 + 9 H3 H1 0 0 1 1 0.055354 0.000000 + 10 O3 OH 0 0 1 1 -0.637433 0.000000 + 11 HO3 HO 0 0 1 1 0.411140 0.000000 + 12 C4 CT 0 0 1 1 0.026886 0.000000 + 13 H4 H1 0 0 1 1 0.207370 0.000000 + 14 O4 OH 0 0 1 1 -0.641959 0.000000 + 15 HO4 HO 0 0 1 1 0.420772 0.000000 + 16 C5 CT 0 0 1 1 0.068030 0.000000 + 17 H5 H1 0 0 1 1 0.095612 0.000000 + 18 C6 CT 0 0 1 1 0.062660 0.000000 + 192H6 H1 0 0 1 1 0.077289 0.000000 + 203H6 H1 0 0 1 1 0.077289 0.000000 + 21 O6 OH 0 0 1 1 -0.677054 0.000000 + 22 HO6 HO 0 0 1 1 0.434974 0.000000 + 1 2 + 1 3 + 1 4 + 3 16 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 8 12 + 10 11 + 12 13 + 12 14 + 12 16 + 14 15 + 16 17 + 16 18 + 18 19 + 18 20 + 18 21 + 21 22 diff --git a/src/data/amber_q/GA2.frg b/src/data/amber_q/GA2.frg new file mode 100644 index 0000000000..a99151c981 --- /dev/null +++ b/src/data/amber_q/GA2.frg @@ -0,0 +1,46 @@ +# This is an automatically generated segment file +# +$GA2 + 21 + 1 C1 AC 3 0 1 1 0.099978 0.000000 + 2 H1 H2 0 0 1 1 0.138270 0.000000 + 3 OR OS 0 0 1 1 -0.406195 0.000000 + 4 C2 CT 0 0 1 1 0.089663 0.000000 + 5 H2 H1 0 0 1 1 0.135805 0.000000 + 6 O2 OG 4 0 1 1 -0.238542 0.000000 + 7 C3 CT 0 0 1 1 0.033403 0.000000 + 8 H3 H1 0 0 1 1 0.187600 0.000000 + 9 O3 OH 0 0 1 1 -0.643404 0.000000 + 10 HO3 HO 0 0 1 1 0.440276 0.000000 + 11 C4 CT 0 0 1 1 0.068168 0.000000 + 12 H4 H1 0 0 1 1 0.135844 0.000000 + 13 O4 OH 0 0 1 1 -0.642604 0.000000 + 14 HO4 HO 0 0 1 1 0.411897 0.000000 + 15 C5 CT 0 0 1 1 0.012908 0.000000 + 16 H5 H1 0 0 1 1 0.129065 0.000000 + 17 C6 CT 0 0 1 1 0.269049 0.000000 + 182H6 H1 0 0 1 1 0.039234 0.000000 + 193H6 H1 0 0 1 1 0.039234 0.000000 + 20 O6 OH 0 0 1 1 -0.708152 0.000000 + 21 HO6 HO 0 0 1 1 0.408503 0.000000 + 1 2 + 1 3 + 1 4 + 3 15 + 4 5 + 4 6 + 4 7 + 7 8 + 7 9 + 7 11 + 9 10 + 11 12 + 11 13 + 11 15 + 13 14 + 15 16 + 15 17 + 17 18 + 17 19 + 17 20 + 20 21 diff --git a/src/data/amber_q/GA3.frg b/src/data/amber_q/GA3.frg new file mode 100644 index 0000000000..7ba4dabab1 --- /dev/null +++ b/src/data/amber_q/GA3.frg @@ -0,0 +1,64 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$GA3 + 29 + 1 C1 AC 3 0 1 1 0.000000 0.000000 + 2 H1 H2 0 0 1 1 0.000000 0.000000 + 3 OR OS 0 0 1 1 -0.300000 0.000000 + 4 C2 CT 0 0 1 1 0.020000 0.000000 + 5 H2 H1 0 0 1 1 0.050000 0.000000 + 6 C3 CT 0 0 1 1 0.250000 0.000000 + 7 H3 H1 0 0 1 1 0.050000 0.000000 + 8 O3 OG 4 0 1 1 -0.300000 0.000000 + 9 C4 CT 0 0 1 1 0.250000 0.000000 + 10 H4 H1 0 0 1 1 0.050000 0.000000 + 11 O4 OG 5 0 1 1 -0.300000 0.000000 + 12 C5 CT 0 0 1 1 0.250000 0.000000 + 13 H5 H1 0 0 1 1 0.050000 0.000000 + 14 C6 CT 0 0 1 1 0.200000 0.000000 + 152H6 H1 0 0 1 1 0.050000 0.000000 + 163H6 H1 0 0 1 1 0.050000 0.000000 + 17 O6 OH 0 0 1 1 -0.490000 0.000000 + 18 HO6 HO 0 0 1 1 0.190000 0.000000 + 19 N N 0 0 1 1 -0.410000 0.000000 + 20 HN H 0 0 1 1 0.270000 0.000000 + 21 CA CT 0 0 1 1 0.020000 0.000000 + 22 HA H1 0 0 1 1 0.050000 0.000000 + 23 CB CT 0 0 1 1 -0.150000 0.000000 + 242HB HC 0 0 1 1 0.050000 0.000000 + 253HB HC 0 0 1 1 0.050000 0.000000 + 264HB HC 0 0 1 1 0.050000 0.000000 + 27 C C 0 1 1 1 0.800000 0.000000 + 28 OC O2 0 0 1 1 -0.900000 0.000000 + 29 O O2 0 0 1 1 -0.900000 0.000000 + 1 2 + 1 3 + 1 4 + 3 12 + 4 5 + 4 6 + 4 19 + 6 7 + 6 8 + 6 9 + 9 10 + 9 11 + 9 12 + 12 13 + 12 14 + 14 15 + 14 16 + 14 17 + 17 18 + 19 20 + 19 21 + 21 22 + 21 23 + 21 27 + 23 24 + 23 25 + 23 26 + 27 28 + 27 29 diff --git a/src/data/amber_q/GAL.frg b/src/data/amber_q/GAL.frg new file mode 100644 index 0000000000..11cb966bdb --- /dev/null +++ b/src/data/amber_q/GAL.frg @@ -0,0 +1,46 @@ +# This is an automatically generated segment file +# +$GAL + 21 + 1 C1 AC 3 0 1 1 -0.181679 0.000000 + 2 H1 H2 0 0 1 1 0.235104 0.000000 + 3 C2 CT 0 0 1 1 0.036346 0.000000 + 4 H2 H1 0 0 1 1 0.149332 0.000000 + 5 O2 OH 0 0 1 1 -0.590556 0.000000 + 6 HO2 HO 0 0 1 1 0.396247 0.000000 + 7 C3 CT 0 0 1 1 0.021948 0.000000 + 8 H3 H1 0 0 1 1 0.115040 0.000000 + 9 O3 OG 4 0 1 1 -0.113637 0.000000 + 10 C4 CT 0 0 1 1 -0.012852 0.000000 + 11 H4 H1 0 0 1 1 0.117350 0.000000 + 12 O4 OH 0 0 1 1 -0.571279 0.000000 + 13 HO4 HO 0 0 1 1 0.390331 0.000000 + 14 C5 CT 0 0 1 1 0.073483 0.000000 + 15 H5 H1 0 0 1 1 0.115195 0.000000 + 16 OR OS 0 0 1 1 -0.218482 0.000000 + 17 C6 CT 0 0 1 1 0.043377 0.000000 + 182H6 H1 0 0 1 1 0.094261 0.000000 + 193H6 H1 0 0 1 1 0.094261 0.000000 + 20 O6 OH 0 0 1 1 -0.568221 0.000000 + 21 HO6 HO 0 0 1 1 0.374431 0.000000 + 1 2 + 1 3 + 1 16 + 3 4 + 3 5 + 3 7 + 5 6 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 + 10 14 + 12 13 + 14 15 + 14 16 + 14 17 + 17 18 + 17 19 + 17 20 + 20 21 diff --git a/src/data/amber_q/GC1.frg b/src/data/amber_q/GC1.frg new file mode 100644 index 0000000000..e798a0be57 --- /dev/null +++ b/src/data/amber_q/GC1.frg @@ -0,0 +1,44 @@ +# This is an automatically generated segment file +# +$GC1 + 20 + 1 OR OS 0 0 1 1 -0.436730 0.000000 + 2 C1 AC 3 0 1 1 0.431092 0.000000 + 3 H1 H2 0 0 1 1 0.016247 0.000000 + 4 C2 CT 0 0 1 1 -0.182335 0.000000 + 5 H2 H1 0 0 1 1 0.149573 0.000000 + 6 N2 N 4 1 1 1 -0.341393 0.000000 + 7 HN H 0 0 1 1 0.236348 0.000000 + 8 C3 CT 0 0 1 1 0.081645 0.000000 + 9 H3 H1 0 0 1 1 0.037446 0.000000 + 10 O3 OS 5 0 1 1 -0.183535 0.000000 + 11 C4 CT 0 0 1 1 0.099460 0.000000 + 12 H4 H1 0 0 1 1 0.152421 0.000000 + 13 O4 OH 0 0 1 1 -0.675942 0.000000 + 14 HO HO 0 0 1 1 0.461259 0.000000 + 15 C5 CT 0 0 1 1 0.105993 0.000000 + 16 H5 H1 0 0 1 1 -0.010713 0.000000 + 17 C6 CT 0 0 1 1 0.149829 0.000000 + 182H6 H1 0 0 1 1 0.054121 0.000000 + 193H6 H1 0 0 1 1 0.054121 0.000000 + 20 O6 OG 6 0 1 1 -0.198907 0.000000 + 1 2 + 1 15 + 2 3 + 2 4 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 8 11 + 11 12 + 11 13 + 11 15 + 13 14 + 15 16 + 15 17 + 17 18 + 17 19 + 17 20 diff --git a/src/data/amber_q/GC2.frg b/src/data/amber_q/GC2.frg new file mode 100644 index 0000000000..31f55b4e8e --- /dev/null +++ b/src/data/amber_q/GC2.frg @@ -0,0 +1,40 @@ +# This is an automatically generated segment file +# +$GC2 + 18 + 1 C1 AC 3 0 1 1 -0.132719 0.000000 + 2 H1 H2 0 0 1 1 0.163584 0.000000 + 3 OR OS 0 0 1 1 -0.201045 0.000000 + 4 C5 CT 0 0 1 1 -0.029468 0.000000 + 5 H5 H1 0 0 1 1 0.155377 0.000000 + 6 C6 CT 0 0 1 1 -0.048733 0.000000 + 72H6 H1 0 0 1 1 0.172392 0.000000 + 83H6 H1 0 0 1 1 0.172392 0.000000 + 9 O6 OG 4 0 1 1 -0.319684 0.000000 + 10 C4 CT 5 0 1 1 -0.205854 0.000000 + 11 H4 H1 0 0 1 1 0.232203 0.000000 + 12 C3 CT 0 0 1 1 0.142364 0.000000 + 13 H3 H1 0 0 1 1 0.127683 0.000000 + 14 O3 OS 6 0 1 1 -0.328735 0.000000 + 15 C2 CT 0 0 1 1 0.037713 0.000000 + 16 H2 H1 0 0 1 1 0.186171 0.000000 + 17 N2 N 7 1 1 1 -0.494259 0.000000 + 18 HN H 0 0 1 1 0.370618 0.000000 + 1 2 + 1 3 + 1 15 + 3 4 + 4 5 + 4 6 + 4 10 + 6 7 + 6 8 + 6 9 + 10 11 + 10 12 + 12 13 + 12 14 + 12 15 + 15 16 + 15 17 + 17 18 diff --git a/src/data/amber_q/GCN.frg b/src/data/amber_q/GCN.frg new file mode 100644 index 0000000000..48db48c854 --- /dev/null +++ b/src/data/amber_q/GCN.frg @@ -0,0 +1,60 @@ +# This is an automatically generated segment file +# +$GCN + 28 + 1 C1 AC 3 0 1 1 -0.296859 0.000000 + 2 H1 H2 0 0 1 1 0.317068 0.000000 + 3 OR OS 0 0 1 1 -0.314059 0.000000 + 4 C2 CT 0 0 1 1 0.023708 0.000000 + 5 H2 H1 0 0 1 1 0.120847 0.000000 + 6 N2 N 0 1 1 1 -0.201785 0.000000 + 7 HN2 H 0 0 1 1 0.235695 0.000000 + 8 C7 C 0 1 1 1 0.402777 0.000000 + 9 O7 O 0 0 1 1 -0.486348 0.000000 + 10 C8 CT 0 0 1 1 -0.142851 0.000000 + 112H8 HC 0 0 1 1 0.050584 0.000000 + 123H8 HC 0 0 1 1 0.050584 0.000000 + 134H8 HC 0 0 1 1 0.050584 0.000000 + 14 C3 CT 0 0 1 1 -0.024602 0.000000 + 15 H3 H1 0 0 1 1 0.108146 0.000000 + 16 O3 OH 0 0 1 1 -0.623229 0.000000 + 17 HO3 HO 0 0 1 1 0.415358 0.000000 + 18 C4 CT 0 0 1 1 0.316496 0.000000 + 19 H4 H1 0 0 1 1 0.059330 0.000000 + 20 O4 OH 0 0 1 1 -0.621120 0.000000 + 21 HO4 HO 0 0 1 1 0.415686 0.000000 + 22 C5 CT 0 0 1 1 0.074395 0.000000 + 23 H5 H1 0 0 1 1 0.057817 0.000000 + 24 C6 CT 0 0 1 1 0.037971 0.000000 + 252H6 H1 0 0 1 1 0.097941 0.000000 + 263H6 H1 0 0 1 1 0.097941 0.000000 + 27 O6 OH 0 0 1 1 -0.558783 0.000000 + 28 HO6 HO 0 0 1 1 0.336708 0.000000 + 1 2 + 1 3 + 1 4 + 3 22 + 4 5 + 4 6 + 4 14 + 6 7 + 6 8 + 8 9 + 8 10 + 10 11 + 10 12 + 10 13 + 14 15 + 14 16 + 14 18 + 16 17 + 18 19 + 18 20 + 18 22 + 20 21 + 22 23 + 22 24 + 24 25 + 24 26 + 24 27 + 27 28 diff --git a/src/data/amber_q/GDP.frg b/src/data/amber_q/GDP.frg new file mode 100644 index 0000000000..e9012037aa --- /dev/null +++ b/src/data/amber_q/GDP.frg @@ -0,0 +1,94 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are obtained from HF 6-31g* +# followed by RESP charge fitting. Charges of equivalent +# atoms are averaged +# +# GDP : Guanosine diphosphate +# +# Prepared by T.P.Straatsma 7/16/99 +# +$GDP + 40 + 1 PB P 0 0 1 1 1.074698 .000000 + 2 O1B O2 0 0 1 1 -.925822 .000000 + 3 O2B O2 0 0 1 1 -.925822 .000000 + 4 O3B O2 0 0 1 1 -.925822 .000000 + 5 O3A OS 0 0 1 1 -.343237 .000000 + 6 PA P 0 0 1 1 1.174128 .000000 + 7 O2A O2 0 0 1 1 -.855657 .000000 + 8 O1A O2 0 0 1 1 -.855657 .000000 + 9 O5* OS 0 0 1 1 -.499273 .000000 + 10 C5* CT 0 0 1 1 .009374 .000000 + 112H5* H1 0 0 1 1 .101660 .000000 + 123H5* H1 0 0 1 1 .101660 .000000 + 13 C4* CT 0 0 1 1 .023226 .000000 + 14 H4* H1 0 0 1 1 .053000 .000000 + 15 O4* OS 0 0 1 1 -.393256 .000000 + 16 C3* CT 0 0 1 1 .471263 .000000 + 17 H3* H1 0 0 1 1 .036811 .000000 + 18 O3* OH 0 0 1 1 -.755512 .000000 + 19 HO3 HO 0 0 1 1 .387701 .000000 + 20 C2* CT 0 0 1 1 .149357 .000000 + 21 H2* H1 0 0 1 1 .138958 .000000 + 22 O2* OH 0 0 1 1 -.688406 .000000 + 23 HO2 HO 0 0 1 1 .409882 .000000 + 24 C1* CT 0 0 1 1 .117387 .000000 + 25 H1* H2 0 0 1 1 .099402 .000000 + 26 N9 N* 0 5 1 1 -.064859 .000000 + 27 C8 CK 0 5 1 1 .240444 .000000 + 28 H8 H5 0 0 1 1 .171277 .000000 + 29 N7 NB 0 5 1 1 -.575569 .000000 + 30 C5 CB 0 11 1 1 .203252 .000000 + 31 C6 C 0 6 1 1 .460522 .000000 + 32 O6 O 0 0 1 1 -.625150 .000000 + 33 N1 NA 0 6 1 1 -.469413 .000000 + 34 H1 H 0 0 1 1 .321419 .000000 + 35 C2 CA 0 6 1 1 .818564 .000000 + 362H2 H 0 0 1 1 .448190 .000000 + 373H2 H 0 0 1 1 .448190 .000000 + 38 N2 N2 0 1 1 1 -1.107937 .000000 + 39 N3 NC 0 6 1 1 -.626702 .000000 + 40 C4 CB 0 11 1 1 .177729 .000000 + 1 2 + 1 3 + 1 4 + 1 5 + 5 6 + 6 7 + 6 8 + 6 9 + 9 10 + 10 11 + 10 12 + 10 13 + 13 14 + 13 15 + 13 16 + 15 24 + 16 17 + 16 18 + 16 20 + 18 19 + 20 21 + 20 22 + 20 24 + 22 23 + 24 25 + 24 26 + 26 27 + 26 40 + 27 28 + 27 29 + 29 30 + 30 31 + 30 40 + 31 32 + 31 33 + 33 34 + 33 35 + 35 38 + 35 39 + 36 38 + 37 38 + 39 40 diff --git a/src/data/amber_q/GL1.frg b/src/data/amber_q/GL1.frg new file mode 100644 index 0000000000..5b5e3ea950 --- /dev/null +++ b/src/data/amber_q/GL1.frg @@ -0,0 +1,44 @@ +# This is an automatically generated segment file +# +$GL1 + 20 + 1 C1 AC 3 0 1 1 -0.005309 0.000000 + 2 H1 H2 0 0 1 1 0.265099 0.000000 + 3 OR OS 0 0 1 1 -0.487694 0.000000 + 4 C2 CT 0 0 1 1 0.121052 0.000000 + 5 H2 H1 0 0 1 1 0.203257 0.000000 + 6 O2 OH 0 0 1 1 -0.767877 0.000000 + 7 HO2 HO 0 0 1 1 0.584113 0.000000 + 8 C3 CT 0 0 1 1 -0.001486 0.000000 + 9 H3 H1 0 0 1 1 0.160825 0.000000 + 10 O3 OG 4 0 1 1 -0.333535 0.000000 + 11 C4 CT 0 0 1 1 0.071732 0.000000 + 12 H4 H1 0 0 1 1 0.107505 0.000000 + 13 O4 OH 0 0 1 1 -0.571075 0.000000 + 14 HO4 HO 0 0 1 1 0.450311 0.000000 + 15 C5 CT 0 0 1 1 0.035653 0.000000 + 16 H5 H1 0 0 1 1 0.086102 0.000000 + 17 C6 CT 0 0 1 1 0.074859 0.000000 + 182H6 H1 0 0 1 1 0.106383 0.000000 + 193H6 H1 0 0 1 1 0.106383 0.000000 + 20 O6 OG 5 0 1 1 -0.206298 0.000000 + 1 2 + 1 3 + 1 4 + 3 15 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 8 11 + 11 12 + 11 13 + 11 15 + 13 14 + 15 16 + 15 17 + 17 18 + 17 19 + 17 20 diff --git a/src/data/amber_q/GL2.frg b/src/data/amber_q/GL2.frg new file mode 100644 index 0000000000..60fe073103 --- /dev/null +++ b/src/data/amber_q/GL2.frg @@ -0,0 +1,44 @@ +# This is an automatically generated segment file +# +$GL2 + 20 + 1 C1 AC 3 0 1 1 -0.014294 0.000000 + 2 H1 H2 0 0 1 1 0.209438 0.000000 + 3 OR OS 0 0 1 1 -0.343306 0.000000 + 4 C2 CT 0 0 1 1 -0.035484 0.000000 + 5 H2 H1 0 0 1 1 0.172160 0.000000 + 6 O2 OG 4 0 1 1 -0.221659 0.000000 + 7 C3 CT 0 0 1 1 0.020232 0.000000 + 8 H3 H1 0 0 1 1 0.174479 0.000000 + 9 O3 OH 0 0 1 1 -0.597323 0.000000 + 10 HO3 HO 0 0 1 1 0.448165 0.000000 + 11 C4 CT 0 0 1 1 0.018125 0.000000 + 12 H4 H1 0 0 1 1 0.148347 0.000000 + 13 O4 OG 5 0 1 1 -0.154442 0.000000 + 14 C5 CT 0 0 1 1 0.079364 0.000000 + 15 H5 H1 0 0 1 1 0.099999 0.000000 + 16 C6 CT 0 0 1 1 -0.040044 0.000000 + 172H6 H1 0 0 1 1 0.115179 0.000000 + 183H6 H1 0 0 1 1 0.115179 0.000000 + 19 O6 OH 0 0 1 1 -0.638046 0.000000 + 20 HO6 HO 0 0 1 1 0.443931 0.000000 + 1 2 + 1 3 + 1 4 + 3 14 + 4 5 + 4 6 + 4 7 + 7 8 + 7 9 + 7 11 + 9 10 + 11 12 + 11 13 + 11 14 + 14 15 + 14 16 + 16 17 + 16 18 + 16 19 + 19 20 diff --git a/src/data/amber_q/GL3.frg b/src/data/amber_q/GL3.frg new file mode 100644 index 0000000000..733de2f236 --- /dev/null +++ b/src/data/amber_q/GL3.frg @@ -0,0 +1,48 @@ +# This is an automatically generated segment file +# +$GL3 + 22 + 1 C1 AC 3 0 1 1 -0.180893 0.000000 + 2 H1 H2 0 0 1 1 0.208778 0.000000 + 3 C2 CT 0 0 1 1 0.125803 0.000000 + 4 H2 H1 0 0 1 1 0.141710 0.000000 + 5 O2 OH 0 0 1 1 -0.611123 0.000000 + 6 HO2 HO 0 0 1 1 0.351163 0.000000 + 7 C3 CT 0 0 1 1 0.260857 0.000000 + 8 H3 H1 0 0 1 1 0.032562 0.000000 + 9 O3 OH 0 0 1 1 -0.666787 0.000000 + 10 HO3 HO 0 0 1 1 0.430357 0.000000 + 11 C4 CT 0 0 1 1 0.082532 0.000000 + 12 H4 H1 0 0 1 1 0.086780 0.000000 + 13 O4 OH 0 0 1 1 -0.646332 0.000000 + 14 HO4 HO 0 0 1 1 0.431530 0.000000 + 15 C5 CT 0 0 1 1 0.035447 0.000000 + 16 H5 H1 0 0 1 1 0.134125 0.000000 + 17 OR OS 0 0 1 1 -0.235957 0.000000 + 18 C6 CT 0 0 1 1 0.103632 0.000000 + 192H6 H1 0 0 1 1 0.074155 0.000000 + 203H6 H1 0 0 1 1 0.074155 0.000000 + 21 O6 OH 0 0 1 1 -0.668207 0.000000 + 22 HO6 HO 0 0 1 1 0.435713 0.000000 + 1 2 + 1 3 + 1 17 + 3 4 + 3 5 + 3 7 + 5 6 + 7 8 + 7 9 + 7 11 + 9 10 + 11 12 + 11 13 + 11 15 + 13 14 + 15 16 + 15 17 + 15 18 + 18 19 + 18 20 + 18 21 + 21 22 diff --git a/src/data/amber_q/GL4.frg b/src/data/amber_q/GL4.frg new file mode 100644 index 0000000000..c3d93dc759 --- /dev/null +++ b/src/data/amber_q/GL4.frg @@ -0,0 +1,48 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$GL4 + 21 + 1 C1 EC 3 0 1 1 0.000000 0.000000 + 2 H1 H2 0 0 1 1 0.000000 0.000000 + 3 OR OS 0 0 1 1 -0.300000 0.000000 + 4 C2 CT 0 0 1 1 0.250000 0.000000 + 5 H2 H1 0 0 1 1 0.050000 0.000000 + 6 O2 OH 0 0 1 1 -0.490000 0.000000 + 7 HO2 HO 0 0 1 1 0.190000 0.000000 + 8 C3 CT 0 0 1 1 0.250000 0.000000 + 9 H3 H1 0 0 1 1 0.050000 0.000000 + 10 O3 OH 0 0 1 1 -0.490000 0.000000 + 11 HO3 HO 0 0 1 1 0.190000 0.000000 + 12 C4 CT 0 0 1 1 0.250000 0.000000 + 13 H4 H1 0 0 1 1 0.050000 0.000000 + 14 O4 OH 0 0 1 1 -0.490000 0.000000 + 15 HO4 HO 0 0 1 1 0.190000 0.000000 + 16 C5 CT 0 0 1 1 0.250000 0.000000 + 17 H5 H1 0 0 1 1 0.050000 0.000000 + 18 C6 CT 0 0 1 1 0.200000 0.000000 + 192H6 H1 0 0 1 1 0.050000 0.000000 + 203H6 H1 0 0 1 1 0.050000 0.000000 + 21 O6 OG 4 0 1 1 -0.300000 0.000000 + 1 2 + 1 3 + 1 4 + 3 16 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 8 12 + 10 11 + 12 13 + 12 14 + 12 16 + 14 15 + 16 17 + 16 18 + 18 19 + 18 20 + 18 21 diff --git a/src/data/amber_q/GL5.frg b/src/data/amber_q/GL5.frg new file mode 100644 index 0000000000..acb1a7fbb5 --- /dev/null +++ b/src/data/amber_q/GL5.frg @@ -0,0 +1,50 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$GL5 + 22 + 1 C1 AC 3 0 1 1 0.000000 0.000000 + 2 H1 H2 0 0 1 1 0.000000 0.000000 + 3 OR OS 0 0 1 1 -0.300000 0.000000 + 4 C2 CT 0 0 1 1 0.250000 0.000000 + 5 H2 H1 0 0 1 1 0.050000 0.000000 + 6 O2 OH 0 0 1 1 -0.490000 0.000000 + 7 HO2 HO 0 0 1 1 0.190000 0.000000 + 8 C3 CT 0 0 1 1 0.250000 0.000000 + 9 H3 H1 0 0 1 1 0.050000 0.000000 + 10 O3 OH 0 0 1 1 -0.490000 0.000000 + 11 HO3 HO 0 0 1 1 0.190000 0.000000 + 12 C4 CT 0 0 1 1 0.250000 0.000000 + 13 H4 H1 0 0 1 1 0.050000 0.000000 + 14 O4 OH 0 0 1 1 -0.490000 0.000000 + 15 HO4 HO 0 0 1 1 0.190000 0.000000 + 16 C5 CT 0 0 1 1 0.250000 0.000000 + 17 H5 H1 0 0 1 1 0.050000 0.000000 + 18 C6 CT 0 0 1 1 0.200000 0.000000 + 192H6 H1 0 0 1 1 0.050000 0.000000 + 203H6 H1 0 0 1 1 0.050000 0.000000 + 21 O6 OH 0 0 1 1 -0.490000 0.000000 + 22 HO6 HO 0 0 1 1 0.190000 0.000000 + 1 2 + 1 3 + 1 4 + 3 16 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 8 12 + 10 11 + 12 13 + 12 14 + 12 16 + 14 15 + 16 17 + 16 18 + 18 19 + 18 20 + 18 21 + 21 22 diff --git a/src/data/amber_q/GL6.frg b/src/data/amber_q/GL6.frg new file mode 100644 index 0000000000..07d3bd730a --- /dev/null +++ b/src/data/amber_q/GL6.frg @@ -0,0 +1,48 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$GL6 + 21 + 1 C1 EC 3 0 1 1 0.000000 0.000000 + 2 H1 H2 0 0 1 1 0.000000 0.000000 + 3 OR OS 0 0 1 1 -0.300000 0.000000 + 4 C2 CT 0 0 1 1 0.250000 0.000000 + 5 H2 H1 0 0 1 1 0.050000 0.000000 + 6 O2 OH 0 0 1 1 -0.490000 0.000000 + 7 HO2 HO 0 0 1 1 0.190000 0.000000 + 8 C3 CT 0 0 1 1 0.250000 0.000000 + 9 H3 H1 0 0 1 1 0.050000 0.000000 + 10 O3 OH 0 0 1 1 -0.490000 0.000000 + 11 HO3 HO 0 0 1 1 0.190000 0.000000 + 12 C4 CT 0 0 1 1 0.250000 0.000000 + 13 H4 H1 0 0 1 1 0.050000 0.000000 + 14 O4 OH 0 0 1 1 -0.490000 0.000000 + 15 HO4 HO 0 0 1 1 0.190000 0.000000 + 16 C5 CT 0 0 1 1 0.250000 0.000000 + 17 H5 H1 0 0 1 1 0.050000 0.000000 + 18 C6 CT 0 0 1 1 0.200000 0.000000 + 19 O6 OG 4 0 1 1 -0.300000 0.000000 + 202H6 H1 0 0 1 1 0.050000 0.000000 + 213H6 H1 0 0 1 1 0.050000 0.000000 + 1 2 + 1 3 + 1 4 + 3 16 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 8 12 + 10 11 + 12 13 + 12 14 + 12 16 + 14 15 + 16 17 + 16 18 + 18 19 + 18 20 + 18 21 diff --git a/src/data/amber_q/GL7.frg b/src/data/amber_q/GL7.frg new file mode 100644 index 0000000000..79086bc7cc --- /dev/null +++ b/src/data/amber_q/GL7.frg @@ -0,0 +1,50 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$GL7 + 22 + 1 C1 AC 3 0 1 1 0.000000 0.000000 + 2 H1 H2 0 0 1 1 0.000000 0.000000 + 3 OR OS 0 0 1 1 -0.300000 0.000000 + 4 C2 CT 0 0 1 1 0.250000 0.000000 + 5 H2 H1 0 0 1 1 0.050000 0.000000 + 6 O2 OH 0 0 1 1 -0.490000 0.000000 + 7 HO2 HO 0 0 1 1 0.190000 0.000000 + 8 C3 CT 0 0 1 1 0.250000 0.000000 + 9 H3 H1 0 0 1 1 0.050000 0.000000 + 10 O3 OH 0 0 1 1 -0.490000 0.000000 + 11 HO3 HO 0 0 1 1 0.190000 0.000000 + 12 C4 CT 0 0 1 1 0.250000 0.000000 + 13 H4 H1 0 0 1 1 0.050000 0.000000 + 14 O4 OH 0 0 1 1 -0.490000 0.000000 + 15 HO4 HO 0 0 1 1 0.190000 0.000000 + 16 C5 CT 0 0 1 1 0.250000 0.000000 + 17 H5 H1 0 0 1 1 0.050000 0.000000 + 18 C6 CT 0 0 1 1 0.200000 0.000000 + 192H6 H1 0 0 1 1 0.050000 0.000000 + 203H6 H1 0 0 1 1 0.050000 0.000000 + 21 O6 OH 0 0 1 1 -0.490000 0.000000 + 22 HO6 HO 0 0 1 1 0.190000 0.000000 + 1 2 + 1 3 + 1 4 + 3 16 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 8 12 + 10 11 + 12 13 + 12 14 + 12 16 + 14 15 + 16 17 + 16 18 + 18 19 + 18 20 + 18 21 + 21 22 diff --git a/src/data/amber_q/GNP.frg b/src/data/amber_q/GNP.frg new file mode 100644 index 0000000000..bc92da23b4 --- /dev/null +++ b/src/data/amber_q/GNP.frg @@ -0,0 +1,104 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are obtained from HF 6-31g* +# followed by RESP charge fitting. Charges of equivalent +# atoms are averaged +# +# GNP : Guanosine imido triphosphate +# +# Prepared by T.P.Straatsma 7/16/99 +# +$GNP + 45 + 1 PG P 0 0 1 1 1.096457 .000000 + 2 O1G O2 0 0 1 1 -.940148 .000000 + 3 O2G O2 0 0 1 1 -.940148 .000000 + 4 O3G O2 0 0 1 1 -.940148 .000000 + 5 N3B N 0 0 1 1 -.769579 .000000 + 6 H3B H 0 0 1 1 .315452 .000000 + 7 PB P 0 0 1 1 1.243377 .000000 + 8 O1B O2 0 0 1 1 -.843182 .000000 + 9 O2B O2 0 0 1 1 -.843182 .000000 + 10 O3A OS 0 0 1 1 -.474613 .000000 + 11 PA P 0 0 1 1 1.171633 .000000 + 12 O2A O2 0 0 1 1 -.843894 .000000 + 13 O1A O2 0 0 1 1 -.843894 .000000 + 14 O5* OS 0 0 1 1 -.451770 .000000 + 15 C5* CT 0 0 1 1 .008623 .000000 + 162H5* H1 0 0 1 1 .104767 .000000 + 173H5* H1 0 0 1 1 .104767 .000000 + 18 C4* CT 0 0 1 1 -.005814 .000000 + 19 H4* H1 0 0 1 1 .061627 .000000 + 20 O4* OS 0 0 1 1 -.391274 .000000 + 21 C3* CT 0 0 1 1 .491472 .000000 + 22 H3* H1 0 0 1 1 .024986 .000000 + 23 O3* OH 0 0 1 1 -.753126 .000000 + 24 HO3 HO 0 0 1 1 .385926 .000000 + 25 C2* CT 0 0 1 1 .152716 .000000 + 26 H2* H1 0 0 1 1 .132748 .000000 + 27 O2* OH 0 0 1 1 -.686327 .000000 + 28 HO2 HO 0 0 1 1 .404134 .000000 + 29 C1* CT 0 0 1 1 .113955 .000000 + 30 H1* H2 0 0 1 1 .100141 .000000 + 31 N9 N* 0 5 1 1 -.068035 .000000 + 32 C8 CK 0 5 1 1 .241741 .000000 + 33 H8 H5 0 0 1 1 .173878 .000000 + 34 N7 NB 0 5 1 1 -.572419 .000000 + 35 C5 CB 0 11 1 1 .197931 .000000 + 36 C6 C 0 6 1 1 .464446 .000000 + 37 O6 O 0 0 1 1 -.629089 .000000 + 38 N1 NA 0 6 1 1 -.474110 .000000 + 39 H1 H 0 0 1 1 .320584 .000000 + 40 C2 CA 0 6 1 1 .821048 .000000 + 412H2 H 0 0 1 1 .446735 .000000 + 423H2 H 0 0 1 1 .446735 .000000 + 43 N2 N2 0 1 1 1 -1.110790 .000000 + 44 N3 NC 0 6 1 1 -.627045 .000000 + 45 C4 CB 0 11 1 1 .182708 .000000 + 1 2 + 1 3 + 1 4 + 1 5 + 5 6 + 5 7 + 7 8 + 7 9 + 7 10 + 10 11 + 11 12 + 11 13 + 11 14 + 14 15 + 15 16 + 15 17 + 15 18 + 18 19 + 18 20 + 18 21 + 20 29 + 21 22 + 21 23 + 21 25 + 23 24 + 25 26 + 25 27 + 25 29 + 27 28 + 29 30 + 29 31 + 31 32 + 31 45 + 32 33 + 32 34 + 34 35 + 35 36 + 35 45 + 36 37 + 36 38 + 38 39 + 38 40 + 40 43 + 40 44 + 41 43 + 42 43 + 44 45 diff --git a/src/data/amber_q/GTP.frg b/src/data/amber_q/GTP.frg new file mode 100644 index 0000000000..c122e55923 --- /dev/null +++ b/src/data/amber_q/GTP.frg @@ -0,0 +1,102 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are obtained from HF 6-31g* +# followed by RESP charge fitting. Charges of equivalent +# atoms are averaged +# +# GTP : Guanosine triphosphate +# +# Prepared by T.P.Straatsma 7/16/99 +# +$GTP + 44 + 1 PG P 0 0 1 1 1.164170 .000000 + 2 O1G O2 0 0 1 1 -.945487 .000000 + 3 O2G O2 0 0 1 1 -.945487 .000000 + 4 O3G O2 0 0 1 1 -.945487 .000000 + 5 PB P 0 0 1 1 1.240313 .000000 + 6 O1B O2 0 0 1 1 -.832996 .000000 + 7 O2B O2 0 0 1 1 -.832996 .000000 + 8 O3B OS 0 0 1 1 -.563773 .000000 + 9 O3A OS 0 0 1 1 -.420057 .000000 + 10 PA P 0 0 1 1 1.145727 .000000 + 11 O2A O2 0 0 1 1 -.834828 .000000 + 12 O1A O2 0 0 1 1 -.834828 .000000 + 13 O5* OS 0 0 1 1 -.473116 .000000 + 14 C5* CT 0 0 1 1 .012341 .000000 + 152H5* H1 0 0 1 1 .107078 .000000 + 163H5* H1 0 0 1 1 .107078 .000000 + 17 C4* CT 0 0 1 1 .003260 .000000 + 18 H4* H1 0 0 1 1 .058872 .000000 + 19 O4* OS 0 0 1 1 -.395391 .000000 + 20 C3* CT 0 0 1 1 .503736 .000000 + 21 H3* H1 0 0 1 1 .024579 .000000 + 22 O3* OH 0 0 1 1 -.757441 .000000 + 23 HO3 HO 0 0 1 1 .386486 .000000 + 24 C2* CT 0 0 1 1 .136824 .000000 + 25 H2* H1 0 0 1 1 .141068 .000000 + 26 O2* OH 0 0 1 1 -.687513 .000000 + 27 HO2 HO 0 0 1 1 .405987 .000000 + 28 C1* CT 0 0 1 1 .119399 .000000 + 29 H1* H2 0 0 1 1 .098283 .000000 + 30 N9 N* 0 5 1 1 -.065470 .000000 + 31 C8 CK 0 5 1 1 .242292 .000000 + 32 H8 H5 0 0 1 1 .173702 .000000 + 33 N7 NB 0 5 1 1 -.574845 .000000 + 34 C5 CB 0 11 1 1 .199400 .000000 + 35 C6 C 0 6 1 1 .463943 .000000 + 36 O6 O 0 0 1 1 -.629076 .000000 + 37 N1 NA 0 6 1 1 -.474598 .000000 + 38 H1 H 0 0 1 1 .320504 .000000 + 39 C2 CA 0 6 1 1 .821481 .000000 + 402H2 H 0 0 1 1 .446858 .000000 + 413H2 H 0 0 1 1 .446858 .000000 + 42 N2 N2 0 1 1 1 -1.111040 .000000 + 43 N3 NC 0 6 1 1 -.626706 .000000 + 44 C4 CB 0 11 1 1 .180896 .000000 + 1 2 + 1 3 + 1 4 + 1 8 + 5 6 + 5 7 + 5 8 + 5 9 + 9 10 + 10 11 + 10 12 + 10 13 + 13 14 + 14 15 + 14 16 + 14 17 + 17 18 + 17 19 + 17 20 + 19 28 + 20 21 + 20 22 + 20 24 + 22 23 + 24 25 + 24 26 + 24 28 + 26 27 + 28 29 + 28 30 + 30 31 + 30 44 + 31 32 + 31 33 + 33 34 + 34 35 + 34 44 + 35 36 + 35 37 + 37 38 + 37 39 + 39 42 + 39 43 + 40 42 + 41 42 + 43 44 diff --git a/src/data/amber_q/HDH.frg b/src/data/amber_q/HDH.frg new file mode 100644 index 0000000000..7c0d353918 --- /dev/null +++ b/src/data/amber_q/HDH.frg @@ -0,0 +1,33 @@ +# This is an automatically generated segment file +# +$HDH + 15 + 1 C1 C 3 1 1 1 0.597879 0.000000 + 2 O1 O 0 0 1 1 -0.656819 0.000000 + 3 C2 CT 0 0 1 1 -0.065272 0.000000 + 42H2 HC 0 0 1 1 0.032636 0.000000 + 53H2 HC 0 0 1 1 0.032636 0.000000 + 6 C3 CT 0 0 1 1 0.378592 0.000000 + 7 H3 H1 0 0 1 1 -0.030998 0.000000 + 8 O3 OH 0 0 1 1 -0.686049 0.000000 + 9 HO3 HO 0 0 1 1 0.397395 0.000000 + 10 C4 CT 0 0 1 1 0.001626 0.000000 + 112H4 HC 0 0 1 1 -0.000813 0.000000 + 123H4 HC 0 0 1 1 -0.000813 0.000000 + 13 C5 CT 4 0 1 1 -0.021174 0.000000 + 142H5 HC 0 0 1 1 0.010587 0.000000 + 153H5 HC 0 0 1 1 0.010587 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 6 + 6 7 + 6 8 + 6 10 + 8 9 + 10 11 + 10 12 + 10 13 + 13 14 + 13 15 diff --git a/src/data/amber_q/HDO.frg b/src/data/amber_q/HDO.frg new file mode 100644 index 0000000000..a1d1b92f27 --- /dev/null +++ b/src/data/amber_q/HDO.frg @@ -0,0 +1,31 @@ +# This is an automatically generated segment file +# +$HDO + 14 + 1 C1 C 3 1 1 1 0.701539 0.000000 + 2 O1 O 0 0 1 1 -0.605368 0.000000 + 3 C2 CT 0 0 1 1 0.029289 0.000000 + 42H2 HC 0 0 1 1 -0.027373 0.000000 + 53H2 HC 0 0 1 1 -0.027373 0.000000 + 6 C3 CT 0 0 1 1 0.003251 0.000000 + 7 H3 H1 0 0 1 1 0.181199 0.000000 + 8 O3 OS 4 0 1 1 -0.305123 0.000000 + 9 C4 CT 0 0 1 1 -0.239938 0.000000 + 102H4 HC 0 0 1 1 0.061761 0.000000 + 113H4 HC 0 0 1 1 0.061761 0.000000 + 12 C5 CT 5 0 1 1 0.202333 0.000000 + 132H5 HC 0 0 1 1 -0.017979 0.000000 + 143H5 HC 0 0 1 1 -0.017979 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 6 + 6 7 + 6 8 + 6 9 + 9 10 + 9 11 + 9 12 + 12 13 + 12 14 diff --git a/src/data/amber_q/HEM.frg b/src/data/amber_q/HEM.frg new file mode 100644 index 0000000000..28e5d52ff1 --- /dev/null +++ b/src/data/amber_q/HEM.frg @@ -0,0 +1,156 @@ +$HEM + 73 + 1FE FE 3 0 1 1 1.740000 0.000000 + 2 N A NP 0 0 1 1 -0.840000 0.000000 + 3 C1A CC 0 4 1 1 0.580000 0.000000 + 4 C2A CB 0 4 1 1 -0.280000 0.000000 + 5 CAA CT 0 0 1 1 -0.100000 0.000000 + 62HAA HC 0 0 1 1 0.100000 0.000000 + 73HAA HC 0 0 1 1 0.100000 0.000000 + 8 CBA CT 0 0 1 1 -0.200000 0.000000 + 92HBA HC 0 0 1 1 0.100000 0.000000 + 103HBA HC 0 0 1 1 0.100000 0.000000 + 11 CGA C 0 1 1 1 0.350000 0.000000 + 12 O1A O2 0 0 1 1 -0.575000 0.000000 + 13 O2A O2 0 0 1 1 -0.575000 0.000000 + 14 C3A CB 0 4 1 1 -0.280000 0.000000 + 15 CMA CT 0 0 1 1 -0.150000 0.000000 + 162HMA HC 0 0 1 1 0.100000 0.000000 + 173HMA HC 0 0 1 1 0.100000 0.000000 + 184HMA HC 0 0 1 1 0.100000 0.000000 + 19 C4A CC 0 4 1 1 0.580000 0.000000 + 20 CHB CD 0 1 1 1 -0.640000 0.000000 + 21 HHB HC 0 0 1 1 0.130000 0.000000 + 22 C1B CC 0 4 1 1 0.580000 0.000000 + 23 N B NO 0 0 1 1 -0.840000 0.000000 + 24 C2B CB 0 4 1 1 -0.280000 0.000000 + 25 CMB CT 0 0 1 1 -0.150000 0.000000 + 262HMB HC 0 0 1 1 0.100000 0.000000 + 273HMB HC 0 0 1 1 0.100000 0.000000 + 284HMB HC 0 0 1 1 0.100000 0.000000 + 29 C3B CB 0 4 1 1 -0.280000 0.000000 + 30 CAB CY 0 0 1 1 -0.100000 0.000000 + 31 HVB HC 0 0 1 1 0.130000 0.000000 + 32 CBB CX 0 0 1 1 -0.200000 0.000000 + 332HV2 HC 0 0 1 1 0.100000 0.000000 + 343HV2 HC 0 0 1 1 0.100000 0.000000 + 35 C4B CC 0 4 1 1 0.580000 0.000000 + 36 CHC CD 0 1 1 1 -0.640000 0.000000 + 37 HHC HC 0 0 1 1 0.130000 0.000000 + 38 C1C CC 0 4 1 1 0.580000 0.000000 + 39 N C NP 0 0 1 1 -0.840000 0.000000 + 40 C2C CB 0 4 1 1 -0.280000 0.000000 + 41 CMC CT 0 0 1 1 -0.150000 0.000000 + 422HMC HC 0 0 1 1 0.100000 0.000000 + 433HMC HC 0 0 1 1 0.100000 0.000000 + 444HMC HC 0 0 1 1 0.100000 0.000000 + 45 C3C CB 0 4 1 1 -0.280000 0.000000 + 46 CAC CY 0 0 1 1 -0.100000 0.000000 + 47 HVC HC 0 0 1 1 0.130000 0.000000 + 48 CBC CX 0 0 1 1 -0.200000 0.000000 + 492HV4 HC 0 0 1 1 0.100000 0.000000 + 503HV4 HC 0 0 1 1 0.100000 0.000000 + 51 C4C CC 0 4 1 1 0.580000 0.000000 + 52 CHD CD 0 1 1 1 -0.640000 0.000000 + 53 HHD HC 0 0 1 1 0.130000 0.000000 + 54 C1D CC 0 4 1 1 0.580000 0.000000 + 55 N D NO 0 0 1 1 -0.840000 0.000000 + 56 C2D CB 0 4 1 1 -0.280000 0.000000 + 57 CMD CT 0 0 1 1 -0.150000 0.000000 + 582HMD HC 0 0 1 1 0.100000 0.000000 + 593HMD HC 0 0 1 1 0.100000 0.000000 + 604HMD HC 0 0 1 1 0.100000 0.000000 + 61 C3D CB 0 4 1 1 -0.280000 0.000000 + 62 C4D CC 0 4 1 1 0.580000 0.000000 + 63 CHA CD 0 1 1 1 -0.640000 0.000000 + 64 HHA HC 0 0 1 1 0.130000 0.000000 + 65 CAD CT 0 0 1 1 -0.100000 0.000000 + 662HAD HC 0 0 1 1 0.100000 0.000000 + 673HAD HC 0 0 1 1 0.100000 0.000000 + 68 CBD CT 0 0 1 1 -0.200000 0.000000 + 692HBD HC 0 0 1 1 0.100000 0.000000 + 703HBD HC 0 0 1 1 0.100000 0.000000 + 71 CGD C 0 1 1 1 0.350000 0.000000 + 72 O1D O2 0 0 1 1 -0.575000 0.000000 + 73 O2D O2 0 0 1 1 -0.575000 0.000000 + 1 2 + 1 23 + 1 39 + 1 55 + 2 3 + 2 19 + 3 4 + 3 63 + 4 5 + 4 14 + 5 6 + 5 7 + 5 8 + 8 9 + 8 10 + 8 11 + 11 12 + 11 13 + 14 15 + 14 19 + 15 16 + 15 17 + 15 18 + 19 20 + 20 21 + 20 22 + 22 23 + 22 24 + 23 35 + 24 25 + 24 29 + 25 26 + 25 27 + 25 28 + 29 30 + 29 35 + 30 31 + 30 32 + 32 33 + 32 34 + 35 36 + 36 37 + 36 38 + 38 39 + 38 40 + 39 51 + 40 41 + 40 45 + 41 42 + 41 43 + 41 44 + 45 46 + 45 51 + 46 47 + 46 48 + 48 49 + 48 50 + 51 52 + 52 53 + 52 54 + 54 55 + 54 56 + 55 62 + 56 57 + 56 61 + 57 58 + 57 59 + 57 60 + 61 62 + 61 65 + 62 63 + 63 64 + 65 66 + 65 67 + 65 68 + 68 69 + 68 70 + 68 71 + 71 72 + 71 73 + diff --git a/src/data/amber_q/HEP.frg b/src/data/amber_q/HEP.frg new file mode 100644 index 0000000000..4d8f4a5445 --- /dev/null +++ b/src/data/amber_q/HEP.frg @@ -0,0 +1,49 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$HEP + 22 + 1 C1 CT 3 0 1 1 -0.100000 0.000000 + 22H1 HC 0 0 1 1 0.050000 0.000000 + 33H1 HC 0 0 1 1 0.050000 0.000000 + 4 C2 CT 0 0 1 1 -0.100000 0.000000 + 52H2 HC 0 0 1 1 0.050000 0.000000 + 63H2 HC 0 0 1 1 0.050000 0.000000 + 7 C3 CT 0 0 1 1 -0.100000 0.000000 + 82H3 HC 0 0 1 1 0.050000 0.000000 + 93H3 HC 0 0 1 1 0.050000 0.000000 + 10 C4 CT 0 0 1 1 -0.100000 0.000000 + 112H4 HC 0 0 1 1 0.050000 0.000000 + 123H4 HC 0 0 1 1 0.050000 0.000000 + 13 C5 CT 0 0 1 1 -0.100000 0.000000 + 142H5 HC 0 0 1 1 0.050000 0.000000 + 153H5 HC 0 0 1 1 0.050000 0.000000 + 16 C6 CT 0 0 1 1 -0.100000 0.000000 + 172H6 HC 0 0 1 1 0.050000 0.000000 + 183H6 HC 0 0 1 1 0.050000 0.000000 + 19 C7 CT 0 0 1 1 -0.150000 0.000000 + 202H7 HC 0 0 1 1 0.050000 0.000000 + 213H7 HC 0 0 1 1 0.050000 0.000000 + 224H7 HC 0 0 1 1 0.050000 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 4 6 + 4 7 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 + 10 13 + 13 14 + 13 15 + 13 16 + 16 17 + 16 18 + 16 19 + 19 20 + 19 21 + 19 22 diff --git a/src/data/amber_q/HP1.frg b/src/data/amber_q/HP1.frg new file mode 100644 index 0000000000..9c99a1cdc8 --- /dev/null +++ b/src/data/amber_q/HP1.frg @@ -0,0 +1,50 @@ +# This is an automatically generated segment file +# +$HP1 + 23 + 1 C1 AC 3 0 1 1 -0.239301 0.000000 + 2 H1 H2 0 0 1 1 0.241979 0.000000 + 3 OR OS 0 0 1 1 -0.415373 0.000000 + 4 C2 CT 0 0 1 1 0.042475 0.000000 + 5 H2 H1 0 0 1 1 0.077985 0.000000 + 6 O2 OH 0 0 1 1 -0.647450 0.000000 + 7 HO2 HO 0 0 1 1 0.482404 0.000000 + 8 C3 CT 0 0 1 1 0.010480 0.000000 + 9 H3 H1 0 0 1 1 0.111498 0.000000 + 10 C4 CT 4 0 1 1 0.436393 0.000000 + 11 H4 H1 0 0 1 1 0.091286 0.000000 + 12 C5 CT 0 0 1 1 0.036980 0.000000 + 13 H5 H1 0 0 1 1 0.127831 0.000000 + 14 C6 CT 0 0 1 1 0.076400 0.000000 + 15 H6 H1 0 0 1 1 0.041079 0.000000 + 16 O6 OH 0 0 1 1 -0.406753 0.000000 + 17 HO6 HO 0 0 1 1 0.097859 0.000000 + 18 C7 CT 0 0 1 1 0.028666 0.000000 + 192H7 H1 0 0 1 1 0.132550 0.000000 + 203H7 H1 0 0 1 1 0.132550 0.000000 + 21 O7 OH 0 0 1 1 -0.668904 0.000000 + 22 HO7 HO 0 0 1 1 0.412396 0.000000 + 23 O3 OG 5 0 1 1 -0.203030 0.000000 + 1 2 + 1 3 + 1 4 + 3 12 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 8 23 + 10 11 + 10 12 + 12 13 + 12 14 + 14 15 + 14 16 + 14 18 + 16 17 + 18 19 + 18 20 + 18 21 + 21 22 diff --git a/src/data/amber_q/HP2.frg b/src/data/amber_q/HP2.frg new file mode 100644 index 0000000000..d52443fa7c --- /dev/null +++ b/src/data/amber_q/HP2.frg @@ -0,0 +1,48 @@ +# This is an automatically generated segment file +# +$HP2 + 22 + 1 C1 AC 3 0 1 1 -0.010164 0.000000 + 2 H1 H2 0 0 1 1 0.240927 0.000000 + 3 OR OS 0 0 1 1 -0.252805 0.000000 + 4 C2 CT 0 0 1 1 -0.006072 0.000000 + 5 H2 H1 0 0 1 1 0.134561 0.000000 + 6 O2 OH 0 0 1 1 -0.610787 0.000000 + 7 HO2 HO 0 0 1 1 0.560263 0.000000 + 8 C3 CT 0 0 1 1 0.033998 0.000000 + 9 H3 H1 0 0 1 1 0.234578 0.000000 + 10 O3 OG 4 0 1 1 -0.082473 0.000000 + 11 C4 CT 5 0 1 1 -0.836484 0.000000 + 12 H4 H1 0 0 1 1 0.429570 0.000000 + 13 C5 CT 0 0 1 1 -0.033855 0.000000 + 14 H5 H1 0 0 1 1 0.246413 0.000000 + 15 C6 CT 0 0 1 1 0.209473 0.000000 + 16 H6 H1 0 0 1 1 0.201307 0.000000 + 17 O6 OH 0 0 1 1 -0.639374 0.000000 + 18 HO6 HO 0 0 1 1 0.424900 0.000000 + 19 C7 CT 0 0 1 1 0.105186 0.000000 + 202H7 H1 0 0 1 1 0.004214 0.000000 + 213H7 H1 0 0 1 1 0.004214 0.000000 + 22 O7 OG 6 0 1 1 -0.357590 0.000000 + 1 2 + 1 3 + 1 4 + 3 13 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 8 11 + 11 12 + 11 13 + 13 14 + 13 15 + 15 16 + 15 17 + 15 19 + 17 18 + 19 20 + 19 21 + 19 22 diff --git a/src/data/amber_q/HP3.frg b/src/data/amber_q/HP3.frg new file mode 100644 index 0000000000..ca78ff65c3 --- /dev/null +++ b/src/data/amber_q/HP3.frg @@ -0,0 +1,56 @@ +# This is an automatically generated segment file +# +$HP3 + 26 + 1 C1 AC 3 0 1 1 -0.181949 0.000000 + 2 H1 H2 0 0 1 1 0.216044 0.000000 + 3 OR OS 0 0 1 1 -0.229481 0.000000 + 4 C2 CT 0 0 1 1 0.277637 0.000000 + 5 H2 H1 0 0 1 1 0.089495 0.000000 + 6 O2 OH 0 0 1 1 -0.894528 0.000000 + 7 HO2 HO 0 0 1 1 0.594996 0.000000 + 8 C3 CT 0 0 1 1 0.029277 0.000000 + 9 H3 H1 0 0 1 1 0.136134 0.000000 + 10 O3 OH 0 0 1 1 -0.774477 0.000000 + 11 HO3 HO 0 0 1 1 0.501260 0.000000 + 12 C4 CT 0 0 1 1 0.451101 0.000000 + 13 H4 H1 0 0 1 1 0.070853 0.000000 + 14 O4 OH 0 0 1 1 -0.974205 0.000000 + 15 HO4 HO 0 0 1 1 0.572360 0.000000 + 16 C5 CT 0 0 1 1 0.055923 0.000000 + 17 H5 H1 0 0 1 1 0.029069 0.000000 + 18 C6 CT 0 0 1 1 0.244883 0.000000 + 19 H6 H1 0 0 1 1 0.089606 0.000000 + 20 O6 OH 0 0 1 1 -0.621510 0.000000 + 21 HO6 HO 0 0 1 1 0.412202 0.000000 + 22 C7 CT 0 0 1 1 0.054009 0.000000 + 232H7 H1 0 0 1 1 0.050176 0.000000 + 243H7 H1 0 0 1 1 0.050176 0.000000 + 25 O7 OH 0 0 1 1 -0.708732 0.000000 + 26 HO7 HO 0 0 1 1 0.459681 0.000000 + 1 2 + 1 3 + 1 4 + 3 16 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 8 12 + 10 11 + 12 13 + 12 14 + 12 16 + 14 15 + 16 17 + 16 18 + 18 19 + 18 20 + 18 22 + 20 21 + 22 23 + 22 24 + 22 25 + 25 26 diff --git a/src/data/amber_q/HP4.frg b/src/data/amber_q/HP4.frg new file mode 100644 index 0000000000..ecd7507d2e --- /dev/null +++ b/src/data/amber_q/HP4.frg @@ -0,0 +1,46 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$HP4 + 20 + 1 C1 AC 0 0 1 1 0.000000 0.000000 + 2 O1 OG 3 0 1 1 0.000000 0.000000 + 3 OR OS 0 0 1 1 -0.300000 0.000000 + 4 C2 CT 4 0 1 1 -0.050000 0.000000 + 5 H2 H2 0 0 1 1 0.000000 0.000000 + 6 C3 CT 0 0 1 1 0.250000 0.000000 + 7 H3 H1 0 0 1 1 0.050000 0.000000 + 8 O3 OH 0 0 1 1 -0.490000 0.000000 + 9 HO3 HO 0 0 1 1 0.190000 0.000000 + 10 C4 CT 5 0 1 1 -0.050000 0.000000 + 11 H4 H1 0 0 1 1 0.050000 0.000000 + 12 O4 OG 6 0 1 1 -0.300000 0.000000 + 13 C5 CT 0 0 1 1 0.250000 0.000000 + 14 H5 H1 0 0 1 1 0.050000 0.000000 + 15 C6 CT 7 0 1 1 -0.050000 0.000000 + 16 H6 H1 0 0 1 1 0.050000 0.000000 + 17 C7 CT 0 0 1 1 0.200000 0.000000 + 182H7 H1 0 0 1 1 0.050000 0.000000 + 193H7 H1 0 0 1 1 0.050000 0.000000 + 20 H7 H1 0 0 1 1 0.050000 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 + 3 13 + 4 6 + 4 7 + 6 10 + 6 11 + 6 12 + 8 9 + 8 17 + 10 13 + 10 14 + 13 15 + 13 16 + 15 17 + 15 20 + 17 18 + 17 19 diff --git a/src/data/amber_q/HP5.frg b/src/data/amber_q/HP5.frg new file mode 100644 index 0000000000..e7c2844637 --- /dev/null +++ b/src/data/amber_q/HP5.frg @@ -0,0 +1,64 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$HP5 + 29 + 1 C1 AC 3 0 1 1 0.000000 0.000000 + 2 H1 H2 0 0 1 1 0.000000 0.000000 + 3 OR OS 0 0 1 1 -0.300000 0.000000 + 4 C2 CT 0 0 1 1 0.250000 0.000000 + 5 H2 H1 0 0 1 1 0.050000 0.000000 + 6 O2 OH 0 0 1 1 -0.490000 0.000000 + 7 HO2 HO 0 0 1 1 0.190000 0.000000 + 8 C3 CT 0 0 1 1 0.250000 0.000000 + 9 H3 H1 0 0 1 1 0.050000 0.000000 + 10 O3 OG 4 0 1 1 -0.300000 0.000000 + 11 C4 CT 0 0 1 1 0.250000 0.000000 + 12 H4 H1 0 0 1 1 0.050000 0.000000 + 13 O4 OH 0 0 1 1 -0.490000 0.000000 + 14 HO4 HO 0 0 1 1 0.190000 0.000000 + 15 C5 CT 0 0 1 1 0.250000 0.000000 + 16 H5 H1 0 0 1 1 0.050000 0.000000 + 17 C6 CT 0 0 1 1 0.250000 0.000000 + 18 H6 H1 0 0 1 1 0.050000 0.000000 + 19 O6 OH 0 0 1 1 -0.490000 0.000000 + 20 HO6 HO 0 0 1 1 0.190000 0.000000 + 21 C7 CT 0 0 1 1 0.200000 0.000000 + 222H7 H1 0 0 1 1 0.050000 0.000000 + 233H7 H1 0 0 1 1 0.050000 0.000000 + 24 OE OS 0 0 1 1 -0.300000 0.000000 + 25 C8 C 0 1 1 1 0.640000 0.000000 + 262H8 H 0 0 1 1 0.270000 0.000000 + 273H8 H 0 0 1 1 0.270000 0.000000 + 28 O81 O 0 0 1 1 -0.570000 0.000000 + 29 N8 N 0 1 1 1 -0.610000 0.000000 + 1 2 + 1 3 + 1 4 + 3 15 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 8 11 + 11 12 + 11 13 + 11 15 + 13 14 + 15 16 + 15 17 + 17 18 + 17 19 + 17 21 + 19 20 + 21 22 + 21 23 + 21 24 + 24 25 + 25 28 + 25 29 + 26 29 + 27 29 diff --git a/src/data/amber_q/HXO.frg b/src/data/amber_q/HXO.frg new file mode 100644 index 0000000000..3082c300e5 --- /dev/null +++ b/src/data/amber_q/HXO.frg @@ -0,0 +1,37 @@ +# This is an automatically generated segment file +# +$HXO + 17 + 1 C1 C 3 1 1 1 0.576548 0.000000 + 2 O1 O2 0 0 1 1 -0.716030 0.000000 + 3 C2 CT 0 0 1 1 0.150222 0.000000 + 42H2 HC 0 0 1 1 -0.005370 0.000000 + 53H2 HC 0 0 1 1 -0.005370 0.000000 + 6 C3 CT 0 0 1 1 0.002475 0.000000 + 72H3 HC 0 0 1 1 -0.001237 0.000000 + 83H3 HC 0 0 1 1 -0.001237 0.000000 + 9 C4 CT 0 0 1 1 0.014959 0.000000 + 102H4 HC 0 0 1 1 -0.007480 0.000000 + 113H4 HC 0 0 1 1 -0.007480 0.000000 + 12 C5 CT 0 0 1 1 0.032564 0.000000 + 132H5 HC 0 0 1 1 -0.016282 0.000000 + 143H5 HC 0 0 1 1 -0.016282 0.000000 + 15 C6 CT 4 0 1 1 0.090772 0.000000 + 162H6 HC 0 0 1 1 -0.045386 0.000000 + 173H6 HC 0 0 1 1 -0.045386 0.000000 + 1 2 + 1 3 + 3 4 + 3 5 + 3 6 + 6 7 + 6 8 + 6 9 + 9 10 + 9 11 + 9 12 + 12 13 + 12 14 + 12 15 + 15 16 + 15 17 diff --git a/src/data/amber_q/IPS.frg b/src/data/amber_q/IPS.frg new file mode 100644 index 0000000000..f05c34eeff --- /dev/null +++ b/src/data/amber_q/IPS.frg @@ -0,0 +1,15 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$IPS + 5 + 1 P P 0 0 1 1 0.000000 0.000000 + 2 O1 O2 0 0 1 1 -0.500000 0.000000 + 3 O2 O2 0 0 1 1 -0.500000 0.000000 + 4 O3 O2 0 0 1 1 -0.500000 0.000000 + 5 O4 O2 0 0 1 1 -0.500000 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 diff --git a/src/data/amber_q/KD1.frg b/src/data/amber_q/KD1.frg new file mode 100644 index 0000000000..ecaa598d6f --- /dev/null +++ b/src/data/amber_q/KD1.frg @@ -0,0 +1,56 @@ +# This is an automatically generated segment file +# +$KD1 + 26 + 1 C1 C 0 1 1 1 0.518979 0.000000 + 2 O1 O 0 0 1 1 -0.508304 0.000000 + 3 O OH 0 0 1 1 -0.279281 0.000000 + 4 HO HO 0 0 1 1 0.360363 0.000000 + 5 OR OS 0 0 1 1 -0.294817 0.000000 + 6 C2 AC 3 0 1 1 0.036168 0.000000 + 7 C3 CT 0 0 1 1 -0.154673 0.000000 + 82H3 HC 0 0 1 1 0.125934 0.000000 + 93H3 HC 0 0 1 1 0.125934 0.000000 + 10 C4 CT 0 0 1 1 -0.065200 0.000000 + 11 H4 H1 0 0 1 1 0.193700 0.000000 + 12 C5 CT 0 0 1 1 0.020912 0.000000 + 13 H5 H1 0 0 1 1 0.171043 0.000000 + 14 C6 CT 0 0 1 1 -0.006439 0.000000 + 15 H6 H1 0 0 1 1 0.128707 0.000000 + 16 C7 CT 0 0 1 1 0.204488 0.000000 + 17 H7 H1 0 0 1 1 0.150785 0.000000 + 18 O7 OH 0 0 1 1 -0.696350 0.000000 + 19 HO7 HO 0 0 1 1 0.472670 0.000000 + 20 C8 CT 0 0 1 1 0.006360 0.000000 + 212H8 H1 0 0 1 1 0.092572 0.000000 + 223H8 H1 0 0 1 1 0.092572 0.000000 + 23 O8 OH 0 0 1 1 -0.659409 0.000000 + 24 HO8 HO 0 0 1 1 0.385334 0.000000 + 25 O4 OG 4 0 1 1 -0.267058 0.000000 + 26 O5 OG 5 0 1 1 -0.154990 0.000000 + 1 2 + 1 3 + 1 6 + 3 4 + 5 6 + 5 14 + 6 7 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 + 10 25 + 12 13 + 12 14 + 12 26 + 14 15 + 14 16 + 16 17 + 16 18 + 16 20 + 18 19 + 20 21 + 20 22 + 20 23 + 23 24 diff --git a/src/data/amber_q/KD2.frg b/src/data/amber_q/KD2.frg new file mode 100644 index 0000000000..319ce6a507 --- /dev/null +++ b/src/data/amber_q/KD2.frg @@ -0,0 +1,58 @@ +# This is an automatically generated segment file +# +$KD2 + 27 + 1 C1 C 0 1 1 1 0.547862 0.000000 + 2 O1 O 0 0 1 1 -0.540830 0.000000 + 3 O OH 0 0 1 1 -0.269611 0.000000 + 4 HO HO 0 0 1 1 0.336841 0.000000 + 5 OR OS 0 0 1 1 -0.338267 0.000000 + 6 C2 CT 3 0 1 1 0.224276 0.000000 + 7 C3 CT 0 0 1 1 -0.099141 0.000000 + 82H3 HC 0 0 1 1 0.092366 0.000000 + 93H3 HC 0 0 1 1 0.092366 0.000000 + 10 C4 CT 0 0 1 1 -0.010965 0.000000 + 11 H4 H1 0 0 1 1 0.109685 0.000000 + 12 C5 CT 0 0 1 1 0.055712 0.000000 + 13 H5 H1 0 0 1 1 -0.152967 0.000000 + 14 O5 OH 0 0 1 1 -0.463618 0.000000 + 15 HO5 HO 0 0 1 1 0.366899 0.000000 + 16 C6 CT 0 0 1 1 -0.055565 0.000000 + 17 H6 H1 0 0 1 1 0.278002 0.000000 + 18 C7 CT 0 0 1 1 0.091959 0.000000 + 19 H7 H1 0 0 1 1 0.178914 0.000000 + 20 O7 OH 0 0 1 1 -1.022990 0.000000 + 21 HO7 HO 0 0 1 1 0.766683 0.000000 + 22 C8 CT 0 0 1 1 0.048311 0.000000 + 232H8 H1 0 0 1 1 0.029467 0.000000 + 243H8 H1 0 0 1 1 0.029467 0.000000 + 25 O8 OH 0 0 1 1 -0.413185 0.000000 + 26 HO8 HO 0 0 1 1 0.337109 0.000000 + 27 O4 OG 4 0 1 1 -0.218780 0.000000 + 1 2 + 1 3 + 1 6 + 3 4 + 5 6 + 5 16 + 6 7 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 + 10 27 + 12 13 + 12 14 + 12 16 + 14 15 + 16 17 + 16 18 + 18 19 + 18 20 + 18 22 + 20 21 + 22 23 + 22 24 + 22 25 + 25 26 diff --git a/src/data/amber_q/KD3.frg b/src/data/amber_q/KD3.frg new file mode 100644 index 0000000000..0cc80c9a0e --- /dev/null +++ b/src/data/amber_q/KD3.frg @@ -0,0 +1,58 @@ +# This is an automatically generated segment file +# +$KD3 + 27 + 1 C1 C 0 1 1 1 1.044383 0.000000 + 2 O1A O2 0 0 1 1 -0.935696 0.000000 + 3 O1B O2 0 0 1 1 -0.935696 0.000000 + 4 OR OS 0 0 1 1 -0.169597 0.000000 + 5 C2 AC 3 0 1 1 0.172224 0.000000 + 6 C3 CT 0 0 1 1 -0.256355 0.000000 + 72H3 HC 0 0 1 1 0.125604 0.000000 + 83H3 HC 0 0 1 1 0.125604 0.000000 + 9 C4 CT 0 0 1 1 0.121398 0.000000 + 10 H4 H1 0 0 1 1 0.084283 0.000000 + 11 O4 OH 0 0 1 1 -0.642891 0.000000 + 12 HO4 HO 0 0 1 1 0.436456 0.000000 + 13 C5 CT 0 0 1 1 0.091253 0.000000 + 14 H5 H1 0 0 1 1 -0.134499 0.000000 + 15 O5 OH 0 0 1 1 -0.594336 0.000000 + 16 HO5 HO 0 0 1 1 0.472890 0.000000 + 17 C6 CT 0 0 1 1 -0.183187 0.000000 + 18 H6 H1 0 0 1 1 0.123957 0.000000 + 19 C7 CT 0 0 1 1 0.086963 0.000000 + 20 H7 H1 0 0 1 1 0.184972 0.000000 + 21 O7 OH 0 0 1 1 -0.332596 0.000000 + 22 HO7 HO 0 0 1 1 0.099128 0.000000 + 23 C8 CT 0 0 1 1 0.141777 0.000000 + 242H8 H1 0 0 1 1 0.052594 0.000000 + 253H8 H1 0 0 1 1 0.052594 0.000000 + 26 O8 OH 0 0 1 1 -0.603639 0.000000 + 27 HO8 HO 0 0 1 1 0.372412 0.000000 + 1 2 + 1 3 + 1 5 + 4 5 + 4 17 + 5 6 + 6 7 + 6 8 + 6 9 + 9 10 + 9 11 + 9 13 + 11 12 + 13 14 + 13 15 + 13 17 + 15 16 + 17 18 + 17 19 + 19 20 + 19 21 + 19 23 + 21 22 + 23 24 + 23 25 + 23 26 + 26 27 diff --git a/src/data/amber_q/KD4.frg b/src/data/amber_q/KD4.frg new file mode 100644 index 0000000000..7f692976c7 --- /dev/null +++ b/src/data/amber_q/KD4.frg @@ -0,0 +1,54 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$KD4 + 24 + 1 C1 C 0 1 1 1 0.800000 0.000000 + 2 O1 O2 0 0 1 1 -0.900000 0.000000 + 3 O O2 0 0 1 1 -0.900000 0.000000 + 4 OR OS 0 0 1 1 -0.300000 0.000000 + 5 C2 AC 3 0 1 1 0.000000 0.000000 + 6 C3 CT 0 0 1 1 -0.100000 0.000000 + 72H3 HC 0 0 1 1 0.050000 0.000000 + 83H3 HC 0 0 1 1 0.050000 0.000000 + 9 C4 CT 0 0 1 1 0.250000 0.000000 + 10 H4 H1 0 0 1 1 0.050000 0.000000 + 11 O4 OG 4 0 1 1 -0.300000 0.000000 + 12 C5 CT 5 0 1 1 -0.050000 0.000000 + 13 H5 H1 0 0 1 1 0.050000 0.000000 + 14 C6 CT 0 0 1 1 0.250000 0.000000 + 15 H6 H1 0 0 1 1 0.050000 0.000000 + 16 C7 CT 0 0 1 1 0.250000 0.000000 + 17 H7 H1 0 0 1 1 0.050000 0.000000 + 18 O7 OH 0 0 1 1 -0.490000 0.000000 + 19 HO7 HO 0 0 1 1 0.190000 0.000000 + 20 C8 CT 0 0 1 1 0.200000 0.000000 + 212H8 H1 0 0 1 1 0.050000 0.000000 + 223H8 H1 0 0 1 1 0.050000 0.000000 + 23 O8 OH 0 0 1 1 -0.490000 0.000000 + 24 HO8 HO 0 0 1 1 0.190000 0.000000 + 1 2 + 1 3 + 1 5 + 4 5 + 4 14 + 5 6 + 6 7 + 6 8 + 6 9 + 9 10 + 9 11 + 9 12 + 12 13 + 12 14 + 14 15 + 14 16 + 16 17 + 16 18 + 16 20 + 18 19 + 20 21 + 20 22 + 20 23 + 23 24 diff --git a/src/data/amber_q/KD5.frg b/src/data/amber_q/KD5.frg new file mode 100644 index 0000000000..09bd593b22 --- /dev/null +++ b/src/data/amber_q/KD5.frg @@ -0,0 +1,60 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$KD5 + 27 + 1 C1 C 0 1 1 1 0.800000 0.000000 + 2 O1 O2 0 0 1 1 -0.900000 0.000000 + 3 O O2 0 0 1 1 -0.900000 0.000000 + 4 OR OS 0 0 1 1 -0.300000 0.000000 + 5 C2 AC 3 0 1 1 0.000000 0.000000 + 6 C3 CT 0 0 1 1 -0.100000 0.000000 + 72H3 HC 0 0 1 1 0.050000 0.000000 + 83H3 HC 0 0 1 1 0.050000 0.000000 + 9 C4 CT 0 0 1 1 0.250000 0.000000 + 10 H4 H1 0 0 1 1 0.050000 0.000000 + 11 O4 OH 0 0 1 1 -0.490000 0.000000 + 12 HO4 HO 0 0 1 1 0.190000 0.000000 + 13 C5 CT 0 0 1 1 0.250000 0.000000 + 14 H5 H1 0 0 1 1 0.050000 0.000000 + 15 O5 OH 0 0 1 1 -0.490000 0.000000 + 16 HO5 HO 0 0 1 1 0.190000 0.000000 + 17 C6 CT 0 0 1 1 0.250000 0.000000 + 18 H6 H1 0 0 1 1 0.050000 0.000000 + 19 C7 CT 0 0 1 1 0.250000 0.000000 + 20 H7 H1 0 0 1 1 0.050000 0.000000 + 21 O7 OH 0 0 1 1 -0.490000 0.000000 + 22 HO7 HO 0 0 1 1 0.190000 0.000000 + 23 C8 CT 0 0 1 1 0.200000 0.000000 + 242H8 H1 0 0 1 1 0.050000 0.000000 + 253H8 H1 0 0 1 1 0.050000 0.000000 + 26 O8 OH 0 0 1 1 -0.490000 0.000000 + 27 HO8 HO 0 0 1 1 0.190000 0.000000 + 1 2 + 1 3 + 1 5 + 4 5 + 4 17 + 5 6 + 6 7 + 6 8 + 6 9 + 9 10 + 9 11 + 9 13 + 11 12 + 13 14 + 13 15 + 13 17 + 15 16 + 17 18 + 17 19 + 19 20 + 19 21 + 19 23 + 21 22 + 23 24 + 23 25 + 23 26 + 26 27 diff --git a/src/data/amber_q/MAN.frg b/src/data/amber_q/MAN.frg new file mode 100644 index 0000000000..e5fe2d58ae --- /dev/null +++ b/src/data/amber_q/MAN.frg @@ -0,0 +1,44 @@ +# This is an automatically generated segment file +# +$MAN + 20 + 1 C1 AC 3 0 1 1 -0.162607 0.000000 + 2 H1 H2 0 0 1 1 0.182851 0.000000 + 3 C2 CT 0 0 1 1 -0.080535 0.000000 + 4 H2 H1 0 0 1 1 0.173175 0.000000 + 5 O2 OG 4 0 1 1 -0.079068 0.000000 + 6 C3 CT 0 0 1 1 0.020952 0.000000 + 7 H3 H1 0 0 1 1 0.156462 0.000000 + 8 C4 CT 0 0 1 1 0.277312 0.000000 + 9 H4 H1 0 0 1 1 0.055141 0.000000 + 10 O4 OH 0 0 1 1 -0.666790 0.000000 + 11 HO4 HO 0 0 1 1 0.440190 0.000000 + 12 C5 CT 0 0 1 1 -0.000761 0.000000 + 13 H5 H1 0 0 1 1 0.105583 0.000000 + 14 OR OS 0 0 1 1 -0.246681 0.000000 + 15 C6 CT 0 0 1 1 0.090569 0.000000 + 162H6 H1 0 0 1 1 0.071777 0.000000 + 173H6 H1 0 0 1 1 0.071777 0.000000 + 18 O6 OH 0 0 1 1 -0.573637 0.000000 + 19 HO6 HO 0 0 1 1 0.359359 0.000000 + 20 O3 OG 5 0 1 1 -0.195069 0.000000 + 1 2 + 1 3 + 1 14 + 3 4 + 3 5 + 3 6 + 6 7 + 6 8 + 6 20 + 8 9 + 8 10 + 8 12 + 10 11 + 12 13 + 12 14 + 12 15 + 15 16 + 15 17 + 15 18 + 18 19 diff --git a/src/data/amber_q/NH4.frg b/src/data/amber_q/NH4.frg new file mode 100644 index 0000000000..19f9488cb8 --- /dev/null +++ b/src/data/amber_q/NH4.frg @@ -0,0 +1,15 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$NH4 + 5 + 1 N N 0 0 1 1 -0.200000 0.000000 + 22H H 0 0 1 1 0.300000 0.000000 + 33H H 0 0 1 1 0.300000 0.000000 + 44H H 0 0 1 1 0.300000 0.000000 + 55H H 0 0 1 1 0.300000 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 diff --git a/src/data/amber_q/Na.sgm b/src/data/amber_q/Na.sgm new file mode 100644 index 0000000000..d962c0a966 --- /dev/null +++ b/src/data/amber_q/Na.sgm @@ -0,0 +1,5 @@ +# This is an automatically generated segment file +# + 1 0 0 0 0 + 1Na Na Na Na 1 1 0 0 + 1.000000 0.000000 1.000000 0.000000 1.000000 0.000000 diff --git a/src/data/amber_q/PET.frg b/src/data/amber_q/PET.frg new file mode 100644 index 0000000000..b729464b84 --- /dev/null +++ b/src/data/amber_q/PET.frg @@ -0,0 +1,37 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$PET + 16 + 1 C1 CT 3 0 1 1 -0.100000 0.000000 + 22H1 HC 0 0 1 1 0.050000 0.000000 + 33H1 HC 0 0 1 1 0.050000 0.000000 + 4 C2 CT 0 0 1 1 -0.100000 0.000000 + 52H2 HC 0 0 1 1 0.050000 0.000000 + 63H2 HC 0 0 1 1 0.050000 0.000000 + 7 C3 CT 0 0 1 1 -0.100000 0.000000 + 82H3 HC 0 0 1 1 0.050000 0.000000 + 93H3 HC 0 0 1 1 0.050000 0.000000 + 10 C4 CT 0 0 1 1 -0.100000 0.000000 + 112H4 HC 0 0 1 1 0.050000 0.000000 + 123H4 HC 0 0 1 1 0.050000 0.000000 + 13 C5 CT 0 0 1 1 -0.150000 0.000000 + 142H5 HC 0 0 1 1 0.050000 0.000000 + 153H5 HC 0 0 1 1 0.050000 0.000000 + 164H5 HC 0 0 1 1 0.050000 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 4 6 + 4 7 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 + 10 13 + 13 14 + 13 15 + 13 16 diff --git a/src/data/amber_q/PNT.frg b/src/data/amber_q/PNT.frg new file mode 100644 index 0000000000..8d73373f2f --- /dev/null +++ b/src/data/amber_q/PNT.frg @@ -0,0 +1,33 @@ +# This is an automatically generated segment file +# +$PNT + 15 + 1 C1 CT 3 0 1 1 0.033906 0.000000 + 22H1 HC 0 0 1 1 -0.016953 0.000000 + 33H1 HC 0 0 1 1 -0.016953 0.000000 + 4 C2 CT 0 0 1 1 0.004668 0.000000 + 52H2 HC 0 0 1 1 -0.002334 0.000000 + 63H2 HC 0 0 1 1 -0.002334 0.000000 + 7 C3 CT 0 0 1 1 0.013981 0.000000 + 82H3 HC 0 0 1 1 -0.006990 0.000000 + 93H3 HC 0 0 1 1 -0.006990 0.000000 + 10 C4 CT 0 0 1 1 0.012201 0.000000 + 112H4 HC 0 0 1 1 -0.006101 0.000000 + 123H4 HC 0 0 1 1 -0.006101 0.000000 + 13 C5 CT 4 0 1 1 0.017278 0.000000 + 142H5 HC 0 0 1 1 -0.008639 0.000000 + 153H5 HC 0 0 1 1 -0.008639 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 4 6 + 4 7 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 + 10 13 + 13 14 + 13 15 diff --git a/src/data/amber_q/PO4.frg b/src/data/amber_q/PO4.frg new file mode 100644 index 0000000000..4946b5e243 --- /dev/null +++ b/src/data/amber_q/PO4.frg @@ -0,0 +1,13 @@ +# This is an automatically generated segment file +# +$PO4 + 5 + 1 OP1 OS 3 0 1 1 -0.139474 0.000000 + 2 P P 0 0 1 1 0.938933 0.000000 + 3 OP2 O2 0 0 1 1 -0.933153 0.000000 + 4 OP3 O2 0 0 1 1 -0.933153 0.000000 + 5 OP4 O2 0 0 1 1 -0.933153 0.000000 + 1 2 + 2 3 + 2 4 + 2 5 diff --git a/src/data/amber_q/PPO.frg b/src/data/amber_q/PPO.frg new file mode 100644 index 0000000000..ada3ac111b --- /dev/null +++ b/src/data/amber_q/PPO.frg @@ -0,0 +1,21 @@ +# This is an automatically generated segment file +# +$PPO + 9 + 1 O11 OS 3 0 1 1 -0.429501 0.000000 + 2 P1 P 0 0 1 1 0.311885 0.000000 + 3 O12 O2 0 0 1 1 -0.490521 0.000000 + 4 O13 O2 0 0 1 1 -0.490521 0.000000 + 5 O14 OS 0 0 1 1 -0.118311 0.000000 + 6 P2 P 0 0 1 1 1.139199 0.000000 + 7 O21 O2 0 0 1 1 -0.755746 0.000000 + 8 O22 O2 0 0 1 1 -0.755746 0.000000 + 9 O23 OS 4 0 1 1 -0.410738 0.000000 + 1 2 + 2 3 + 2 4 + 2 5 + 5 6 + 6 7 + 6 8 + 6 9 diff --git a/src/data/amber_q/RH2.frg b/src/data/amber_q/RH2.frg new file mode 100644 index 0000000000..8f530abff1 --- /dev/null +++ b/src/data/amber_q/RH2.frg @@ -0,0 +1,46 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$RH2 + 20 + 1 C1 AC 3 0 1 1 0.000000 0.000000 + 2 H1 H2 0 0 1 1 0.000000 0.000000 + 3 OR OS 0 0 1 1 -0.300000 0.000000 + 4 C2 CT 0 0 1 1 0.250000 0.000000 + 5 H2 H1 0 0 1 1 0.050000 0.000000 + 6 O2 OG 4 0 1 1 -0.300000 0.000000 + 7 C3 CT 0 0 1 1 0.250000 0.000000 + 8 H3 H1 0 0 1 1 0.050000 0.000000 + 9 O3 OH 0 0 1 1 -0.490000 0.000000 + 10 HO3 HO 0 0 1 1 0.190000 0.000000 + 11 C4 CT 0 0 1 1 0.250000 0.000000 + 12 H4 H1 0 0 1 1 0.050000 0.000000 + 13 O4 OH 0 0 1 1 -0.490000 0.000000 + 14 HO4 HO 0 0 1 1 0.190000 0.000000 + 15 C5 CT 0 0 1 1 0.250000 0.000000 + 16 H5 H1 0 0 1 1 0.050000 0.000000 + 17 C6 CT 0 0 1 1 -0.150000 0.000000 + 182H6 HC 0 0 1 1 0.050000 0.000000 + 193H6 HC 0 0 1 1 0.050000 0.000000 + 204H6 HC 0 0 1 1 0.050000 0.000000 + 1 2 + 1 3 + 1 4 + 3 15 + 4 5 + 4 6 + 4 7 + 7 8 + 7 9 + 7 11 + 9 10 + 11 12 + 11 13 + 11 15 + 13 14 + 15 16 + 15 17 + 17 18 + 17 19 + 17 20 diff --git a/src/data/amber_q/RHA.frg b/src/data/amber_q/RHA.frg new file mode 100644 index 0000000000..d16ebc0a22 --- /dev/null +++ b/src/data/amber_q/RHA.frg @@ -0,0 +1,44 @@ +# This is an automatically generated segment file +# +$RHA + 20 + 1 C1 AC 3 0 1 1 -0.362918 0.000000 + 2 H1 H2 0 0 1 1 0.338065 0.000000 + 3 C2 CT 0 0 1 1 0.081671 0.000000 + 4 H2 H1 0 0 1 1 0.117337 0.000000 + 5 O2 OH 0 0 1 1 -0.580083 0.000000 + 6 HO2 HO 0 0 1 1 0.420095 0.000000 + 7 C3 CT 0 0 1 1 0.055135 0.000000 + 8 H3 H1 0 0 1 1 0.089139 0.000000 + 9 O3 OH 0 0 1 1 -0.613470 0.000000 + 10 HO3 HO 0 0 1 1 0.429006 0.000000 + 11 C4 CT 0 0 1 1 0.090177 0.000000 + 12 H4 H1 0 0 1 1 0.199352 0.000000 + 13 O4 OG 4 0 1 1 -0.206307 0.000000 + 14 C5 CT 0 0 1 1 0.091230 0.000000 + 15 H5 H1 0 0 1 1 0.074855 0.000000 + 16 OR OS 0 0 1 1 -0.233814 0.000000 + 17 C6 CT 0 0 1 1 -0.204654 0.000000 + 182H6 HC 0 0 1 1 0.071728 0.000000 + 193H6 HC 0 0 1 1 0.071728 0.000000 + 204H6 HC 0 0 1 1 0.071728 0.000000 + 1 2 + 1 3 + 1 16 + 3 4 + 3 5 + 3 7 + 5 6 + 7 8 + 7 9 + 7 11 + 9 10 + 11 12 + 11 13 + 11 14 + 14 15 + 14 16 + 14 17 + 17 18 + 17 19 + 17 20 diff --git a/src/data/amber_q/SO4.frg b/src/data/amber_q/SO4.frg new file mode 100644 index 0000000000..f8be6673e3 --- /dev/null +++ b/src/data/amber_q/SO4.frg @@ -0,0 +1,15 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude guestimations +# +$SO4 + 5 + 1 S S 0 0 1 1 0.000000 0.000000 + 2 O1 O2 0 0 1 1 -0.500000 0.000000 + 3 O2 O2 0 0 1 1 -0.500000 0.000000 + 4 O3 O2 0 0 1 1 -0.500000 0.000000 + 5 O4 O2 0 0 1 1 -0.500000 0.000000 + 1 2 + 1 3 + 1 4 + 1 5 diff --git a/src/data/amber_q/amber.par b/src/data/amber_q/amber.par new file mode 100644 index 0000000000..d36a26df1e --- /dev/null +++ b/src/data/amber_q/amber.par @@ -0,0 +1,137 @@ +This is the AMBER96 user defined parameter file for NWChem 3.2 and ARGOS 7.0 +Electrostatic 1-4 scaling factor 0.833333 +Relative dielectric constant 1.000000 +Parameters epsilon R* +Atoms +Ne 20.17900 3.16779E-01 1.55006E-01 1 1111111111 + 10 1.58389E-01 1.55006E-01 TPS000106 JCP 85, 6720-6727 (1986) +Li 6.94000 6.18572E-02 1.44006E-01 1 1111111111 + 3 3.09286E-02 1.44006E-01 +Na 22.98977 6.18572E-02 1.44006E-01 1 1111111111 + 11 3.09286E-02 1.44006E-01 TPS 890621 +Mg 24.30500 4.30952E-02 1.36000E-01 1 1111111111 + 12 2.15476E-02 1.36000E-01 TPS000106 JCC 12, 1125-1128 (1991) +K 39.10000 1.37235E-03 2.65800E-01 1 1111111111 + 19 6.86175E-04 2.65800E-01 +Ca 40.08000 3.78520E-02 1.74000E-01 1 1111111111 + 20 1.89260E-02 1.74000E-01 TPS000106 JCC 12, 1125-1128 (1991) +Rb 85.47000 7.11278E-04 2.95600E-01 1 1111111111 + 37 3.55639E-04 2.95600E-01 +Sr 87.62000 2.70286E-01 1.92000E-01 1 1111111111 + 38 1.35143E-01 1.92000E-01 TPS000106 JCC 12, 1125-1128 (1991) +Cs 132.91000 3.37229E-04 3.39500E-01 1 1111111111 + 55 1.68614E-04 3.39500E-01 +Cl 35.45300 4.44950E-01 2.50000E-01 1 1111111111 + 17 2.22475E-01 2.50000E-01 +FE 55.00000 0.00000E+00 0.00000E+00 1 1111111111 + 26 0.00000E+00 0.00000E+00 +CD 12.01100 3.59820E-01 1.90800E-01 1 1111111111 + 6 1.79910E-01 1.90800E-01 +CY 12.01100 3.59820E-01 1.90800E-01 1 1111111111 + 6 1.79910E-01 1.90800E-01 +CX 12.01100 3.59820E-01 1.90800E-01 1 1111111111 + 6 1.79910E-01 1.90800E-01 +NO 14.00674 7.11283E-01 1.82400E-01 1 1111111111 + 7 3.55641E-01 1.82400E-01 +NP 14.00674 7.11283E-01 1.82400E-01 1 1111111111 + 7 3.55641E-01 1.82400E-01 +Cross +Bonds +FE -NO 0.20100 4.18400E+04 +FE -NP 0.20100 4.18400E+04 +CC -NP 0.13840 2.64429E+05 +CB -CC 0.14440 2.28446E+05 +CC -CD 0.13910 3.27189E+05 +CB -CT 0.15010 2.48530E+05 +HC -CD 0.10900 2.82838E+05 +CC -NO 0.13840 2.64429E+05 +CB -CY 0.15010 2.48530E+05 +HC -CY 0.10900 2.84512E+05 +CX -CY 0.13400 4.76976E+05 +HC -CX 0.10900 2.84512E+05 +Angles +CB -CB -CC 1.86750 5.85760E+02 +CB -CB -CT 2.23751 5.85760E+02 +CB -CB -CY 2.23751 5.85760E+02 +CB -CC -CD 2.18864 5.85760E+02 +CB -CC -NO 1.92510 5.85760E+02 +CB -CC -NP 1.92510 5.85760E+02 +CD -CC -NO 2.19039 5.85760E+02 +CD -CC -NP 2.19039 5.85760E+02 +CC -CB -CT 2.17992 5.85760E+02 +CC -CB -CY 2.17992 5.85760E+02 +HC -CD -CC 2.05949 2.51040E+02 +CC -CD -CC 2.16595 5.85760E+02 +HC -CT -CB 1.91114 2.92880E+02 +CB -CT -CT 1.98968 5.27184E+02 +CT -CT -Cl 1.91986 3.55810E+02 +Cl -CT -Cl 1.94604 4.18600E+02 +HC -CX -HC 2.09440 2.92880E+02 +HC -CX -CY 2.09440 2.92880E+02 +HC -CY -CB 2.09440 2.92880E+02 +HC -CY -CX 2.09440 2.92880E+02 +CB -CY -CX 2.09440 5.85760E+02 +CC -NO -CC 1.83958 5.85760E+02 +CC -NO -FE 2.22355 2.51040E+02 +CC -NP -CC 1.83958 5.85760E+02 +CC -NP -FE 2.22355 2.51040E+02 +NB -FE -NO 1.57080 4.18400E+02 +NB -FE -NP 1.57080 4.18400E+02 +NO -FE -NO 1.57080 0.00000E+00 +NO -FE -NP 1.57080 4.18400E+02 +NP -FE -NP 1.57080 0.00000E+00 +N2 -CA -CT 2.09440 5.85760E+02 !taken from N2 -CA N2; RDL 07/31/00 +Proper dihedrals + -NB -FE - 0.00000 0.00000E+02 2 + -NO -FE - 3.14159 0.00000E+02 2 + -NP -FE - 3.14159 0.00000E+02 2 + -CB -CC - 3.14159 3.29490E+00 2 + -CB -CT - 3.14159 0.00000E+00 2 + -CB -CY - 3.14159 0.00000E+00 2 + -CC -CD - 3.14159 8.26340E+00 2 + -CC -NO - 3.14159 5.96220E+00 2 + -CC -NP - 3.14159 5.96220E+00 2 + -CX -CY - 3.14159 3.13800E+01 2 +Improper dihedrals + - -CC -CC 3.14159 4.18400E+00 2 + - -CC -CB 3.14159 4.18400E+00 2 + - -CB -NP 3.14159 4.18400E+00 2 + - -CB -NO 3.14159 4.18400E+00 2 + - -CB -CY 3.14159 4.18400E+00 2 + - -CB -CT 3.14159 4.18400E+00 2 + - -CD -HC 3.14159 4.18400E+00 2 +Atom types +Li 3 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +Na 11 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +Mg 12 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +K 19 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +Ca 20 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +Rb 37 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +Sr 38 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +# +Cl 17 0 0 0 0 0 0 0 0 0 + 0 0 0 0 0 + 0 0 0 0 0 +O2 8 0 0 0 1 15 4 808 1808 800 + 0 0 0 0 0 + 0 0 0 0 0 diff --git a/src/data/amber_q/coc.frg b/src/data/amber_q/coc.frg new file mode 100644 index 0000000000..c915212040 --- /dev/null +++ b/src/data/amber_q/coc.frg @@ -0,0 +1,13 @@ +# Fragment definition for crown ether fragment -CH2-O-CH2- +$coc + 7 + 1 C1 CT 3 0 1 1 0.000000 0.000000 + 22H1 H1 0 0 1 1 0.150000 0.000000 + 33H1 H1 0 0 1 1 0.150000 0.000000 + 4 O OS 0 0 1 1 -0.600000 0.000000 + 5 C2 CT 4 0 1 1 0.000000 0.000000 + 62H2 H1 0 0 1 1 0.150000 0.000000 + 73H2 H1 0 0 1 1 0.150000 0.000000 + 1 4 5 + 2 1 3 + 6 5 7 diff --git a/src/data/amber_q/etl.frg b/src/data/amber_q/etl.frg new file mode 100644 index 0000000000..a2f4801b35 --- /dev/null +++ b/src/data/amber_q/etl.frg @@ -0,0 +1,17 @@ +# Fragment definition for ethanol +$ethanol + 9 + 1 C1 CT 0 0 1 1 -0.180000 0.000000 + 22H1 HC 0 0 1 1 0.060000 0.000000 + 33H1 HC 0 0 1 1 0.060000 0.000000 + 44H1 HC 0 0 1 1 0.060000 0.000000 + 5 C2 CT 0 0 1 1 -0.032000 0.000000 + 62H2 H1 0 0 1 1 0.148500 0.000000 + 73H2 H1 0 0 1 1 0.148500 0.000000 + 8 O OH 0 0 1 1 -0.700000 0.000000 + 9 H HO 0 0 1 1 0.435000 0.000000 + 2 1 3 + 4 1 5 8 9 + 6 5 7 + +