diff --git a/src/data/amber_q/lps_ec/BU1.frg b/src/data/amber_q/lps_ec/BU1.frg new file mode 100644 index 0000000000..1cf9d5b9cb --- /dev/null +++ b/src/data/amber_q/lps_ec/BU1.frg @@ -0,0 +1,34 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 10:35:31 +# +$BU1 + 13 1 1 0 +BU1 + 1 C1 CT 3 0 0 1 1 -0.864254 0.000000 + 22H1 HC 0 0 0 1 1 0.349875 0.000000 + 33H1 HC 0 0 0 1 1 0.349875 0.000000 + 4 C2 CT 0 0 0 1 1 -0.223449 0.000000 + 52H2 HC 0 0 0 1 1 0.185394 0.000000 + 63H2 HC 0 0 0 1 1 0.185394 0.000000 + 7 C3 CT 0 0 0 1 1 -0.091103 0.000000 + 82H3 HC 0 0 0 1 1 0.019263 0.000000 + 93H3 HC 0 0 0 1 1 0.019263 0.000000 + 10 C4 CT 0 0 0 1 1 -0.066351 0.000000 + 112H4 HC 0 0 0 1 1 0.045364 0.000000 + 123H4 HC 0 0 0 1 1 0.045364 0.000000 + 134H4 HC 0 0 0 1 1 0.045364 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 4 6 + 4 7 + 7 8 + 7 9 + 7 10 + 10 11 + 10 12 + 10 13 diff --git a/src/data/amber_q/lps_ec/BU2.frg b/src/data/amber_q/lps_ec/BU2.frg new file mode 100644 index 0000000000..b61690e81f --- /dev/null +++ b/src/data/amber_q/lps_ec/BU2.frg @@ -0,0 +1,32 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 10:35:31 +# +$BU2 + 12 1 1 0 +BU2 + 1 C1 CT 3 0 0 1 1 -0.263991 0.000000 + 22H1 HC 0 0 0 1 1 0.073152 0.000000 + 33H1 HC 0 0 0 1 1 0.073152 0.000000 + 4 C2 CT 0 0 0 1 1 0.035826 0.000000 + 52H2 HC 0 0 0 1 1 -0.119366 0.000000 + 63H2 HC 0 0 0 1 1 -0.119366 0.000000 + 7 C3 CT 0 0 0 1 1 0.107797 0.000000 + 82H3 HC 0 0 0 1 1 -0.024820 0.000000 + 93H3 HC 0 0 0 1 1 -0.024820 0.000000 + 10 C4 CT 4 0 0 1 1 -0.195478 0.000000 + 112H4 HC 0 0 0 1 1 0.228957 0.000000 + 123H4 HC 0 0 0 1 1 0.228957 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/lps_ec/GA1.frg b/src/data/amber_q/lps_ec/GA1.frg new file mode 100644 index 0000000000..5c27f05742 --- /dev/null +++ b/src/data/amber_q/lps_ec/GA1.frg @@ -0,0 +1,55 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 10:35:31 +# +$GA1 + 23 1 1 0 +GA1 + 1 C1 AC 0 0 0 1 1 0.193194 0.000000 + 2 H1 H2 0 0 0 1 1 0.072590 0.000000 + 3 O1 OS 3 0 0 1 1 -0.087662 0.000000 + 4 C2 CT 0 0 0 1 1 0.299004 0.000000 + 5 H2 H1 0 0 0 1 1 0.069050 0.000000 + 6 O2 OH 0 0 0 1 1 -0.807938 0.000000 + 7 HO2 HO 0 0 0 1 1 0.452336 0.000000 + 8 C3 CT 0 0 0 1 1 0.726424 0.000000 + 9 H3 H1 0 0 0 1 1 -0.083389 0.000000 + 10 O3 OH 0 0 0 1 1 -1.291508 0.000000 + 11 HO3 HO 0 0 0 1 1 0.630135 0.000000 + 12 C4 CT 0 0 0 1 1 0.056284 0.000000 + 13 H4 H1 0 0 0 1 1 0.301851 0.000000 + 14 O4 OH 0 0 0 1 1 -1.000961 0.000000 + 15 HO4 HO 0 0 0 1 1 0.556479 0.000000 + 16 C5 CT 0 0 0 1 1 0.236298 0.000000 + 17 H5 H1 0 0 0 1 1 0.075909 0.000000 + 18 C6 CT 0 0 0 1 1 0.278215 0.000000 + 192H6 H1 0 0 0 1 1 0.092913 0.000000 + 203H6 H1 0 0 0 1 1 0.092913 0.000000 + 21 O6 OH 0 0 0 1 1 -0.759032 0.000000 + 22 HO6 HO 0 0 0 1 1 0.417351 0.000000 + 23 OR OS 0 0 0 1 1 -0.521455 0.000000 + 1 2 + 1 3 + 1 4 + 1 23 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 8 12 + 10 11 + 12 13 + 12 14 + 12 16 + 14 15 + 16 17 + 16 18 + 16 23 + 18 19 + 18 20 + 18 21 + 21 22 diff --git a/src/data/amber_q/lps_ec/GL1.frg b/src/data/amber_q/lps_ec/GL1.frg new file mode 100644 index 0000000000..ee054b09a9 --- /dev/null +++ b/src/data/amber_q/lps_ec/GL1.frg @@ -0,0 +1,47 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 10:35:31 +# +$GL1 + 19 1 1 0 +GL1 + 1 C1 AC 0 0 0 1 1 0.183946 0.000000 + 2 H1 H2 0 0 0 1 1 0.092269 0.000000 + 3 O1 OS 3 0 0 1 1 0.142115 0.000000 + 4 C2 CT 0 0 0 1 1 0.487700 0.000000 + 5 H2 H1 0 0 0 1 1 0.063090 0.000000 + 6 O2 OH 0 0 0 1 1 -1.053101 0.000000 + 7 HO2 HO 0 0 0 1 1 0.554009 0.000000 + 8 C3 CT 4 0 0 1 1 -0.301894 0.000000 + 9 H3 H1 0 0 0 1 1 0.098353 0.000000 + 10 C4 CT 0 0 0 1 1 0.606714 0.000000 + 11 H4 H1 0 0 0 1 1 -0.060495 0.000000 + 12 O4 OH 0 0 0 1 1 -0.833144 0.000000 + 13 HO4 HO 0 0 0 1 1 0.425334 0.000000 + 14 C5 CT 0 0 0 1 1 0.404266 0.000000 + 15 H5 H1 0 0 0 1 1 -0.166015 0.000000 + 16 C6 CT 5 0 0 1 1 -0.375243 0.000000 + 172H6 H1 0 0 0 1 1 0.142981 0.000000 + 183H6 H1 0 0 0 1 1 0.142981 0.000000 + 19 OR OS 0 0 0 1 1 -0.553867 0.000000 + 1 2 + 1 3 + 1 4 + 1 19 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 10 11 + 10 12 + 10 14 + 12 13 + 14 15 + 14 16 + 14 19 + 16 17 + 16 18 diff --git a/src/data/amber_q/lps_ec/GL2.frg b/src/data/amber_q/lps_ec/GL2.frg new file mode 100644 index 0000000000..34bed8264c --- /dev/null +++ b/src/data/amber_q/lps_ec/GL2.frg @@ -0,0 +1,51 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 10:35:31 +# +$GL2 + 21 1 1 0 +GL2 + 1 C1 AC 0 0 0 1 1 0.509726 0.000000 + 2 H1 H2 0 0 0 1 1 0.133252 0.000000 + 3 O1 OS 3 0 0 1 1 -0.231396 0.000000 + 4 C2 CT 4 0 0 1 1 -0.469045 0.000000 + 5 H2 H1 0 0 0 1 1 0.168614 0.000000 + 6 C3 CT 0 0 0 1 1 0.680179 0.000000 + 7 H3 H1 0 0 0 1 1 -0.069090 0.000000 + 8 O3 OH 0 0 0 1 1 -0.871026 0.000000 + 9 HO3 HO 0 0 0 1 1 0.465673 0.000000 + 10 C4 CT 0 0 0 1 1 0.305521 0.000000 + 11 H4 H1 0 0 0 1 1 0.099451 0.000000 + 12 O4 OH 0 0 0 1 1 -0.948886 0.000000 + 13 HO4 HO 0 0 0 1 1 0.531024 0.000000 + 14 C5 CT 0 0 0 1 1 0.419333 0.000000 + 15 H5 H1 0 0 0 1 1 0.004956 0.000000 + 16 C6 CT 0 0 0 1 1 0.267679 0.000000 + 172H6 H1 0 0 0 1 1 -0.031244 0.000000 + 183H6 H1 0 0 0 1 1 -0.031244 0.000000 + 19 O6 OH 0 0 0 1 1 -0.812945 0.000000 + 20 HO6 HO 0 0 0 1 1 0.486555 0.000000 + 21 OR OS 0 0 0 1 1 -0.607087 0.000000 + 1 2 + 1 3 + 1 4 + 1 21 + 4 5 + 4 6 + 6 7 + 6 8 + 6 10 + 8 9 + 10 11 + 10 12 + 10 14 + 12 13 + 14 15 + 14 16 + 14 21 + 16 17 + 16 18 + 16 19 + 19 20 diff --git a/src/data/amber_q/lps_ec/GL3.frg b/src/data/amber_q/lps_ec/GL3.frg new file mode 100644 index 0000000000..bd50437483 --- /dev/null +++ b/src/data/amber_q/lps_ec/GL3.frg @@ -0,0 +1,51 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 10:35:31 +# +$GL3 + 21 1 1 0 +GL3 + 1 C1 AC 0 0 0 1 1 0.573279 0.000000 + 2 H1 H2 0 0 0 1 1 0.108300 0.000000 + 3 O1 OS 3 0 0 1 1 -0.306364 0.000000 + 4 C2 CT 0 0 0 1 1 0.177942 0.000000 + 5 H2 H1 0 0 0 1 1 0.092618 0.000000 + 6 O2 OH 0 0 0 1 1 -0.718049 0.000000 + 7 HO2 HO 0 0 0 1 1 0.415211 0.000000 + 8 C3 CT 0 0 0 1 1 0.325435 0.000000 + 9 H3 H1 0 0 0 1 1 0.076482 0.000000 + 10 O3 OH 0 0 0 1 1 -0.795236 0.000000 + 11 HO3 HO 0 0 0 1 1 0.464025 0.000000 + 12 C4 CT 0 0 0 1 1 0.170032 0.000000 + 13 H4 H1 0 0 0 1 1 -0.033343 0.000000 + 14 O4 OH 0 0 0 1 1 -0.688254 0.000000 + 15 HO4 HO 0 0 0 1 1 0.325372 0.000000 + 16 C5 CT 0 0 0 1 1 0.633759 0.000000 + 17 H5 H1 0 0 0 1 1 0.006036 0.000000 + 18 C6 CT 4 0 0 1 1 -0.248292 0.000000 + 192H6 H1 0 0 0 1 1 0.101066 0.000000 + 203H6 H1 0 0 0 1 1 0.101066 0.000000 + 21 OR OS 0 0 0 1 1 -0.781085 0.000000 + 1 2 + 1 3 + 1 4 + 1 21 + 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 + 16 21 + 18 19 + 18 20 diff --git a/src/data/amber_q/lps_ec/GN1.frg b/src/data/amber_q/lps_ec/GN1.frg new file mode 100644 index 0000000000..c7f3b5792b --- /dev/null +++ b/src/data/amber_q/lps_ec/GN1.frg @@ -0,0 +1,55 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 08:58:30 +# +$GN1 + 23 1 1 0 +GN1 + 1 C1 AC 3 0 0 1 1 0.113419 0.000000 + 2 H1 H2 0 0 0 1 1 0.072233 0.000000 + 3 C2 CT 0 0 0 1 1 -0.186703 0.000000 + 4 H2 H1 0 0 0 1 1 0.430869 0.000000 + 5 N N 0 1 0 1 1 -0.216291 0.000000 + 6 H H 0 0 0 1 1 0.150137 0.000000 + 7 C C 4 1 0 1 1 0.491961 0.000000 + 8 O O 0 0 0 1 1 -0.699036 0.000000 + 9 C3 CT 0 0 0 1 1 0.071114 0.000000 + 10 H3 H1 0 0 0 1 1 0.257830 0.000000 + 11 O3 OS 0 0 0 1 1 -0.660668 0.000000 + 12 C31 C 5 1 0 1 1 0.838466 0.000000 + 13 O31 O 0 0 0 1 1 -0.660802 0.000000 + 14 C4 CT 0 0 0 1 1 -.1417480 0.000000 + 15 H4 H1 0 0 0 1 1 0.358553 0.000000 + 16 O4 OH 0 0 0 1 1 -0.891694 0.000000 + 17 HO4 HO 0 0 0 1 1 0.512610 0.000000 + 18 C5 CT 0 0 0 1 1 0.490790 0.000000 + 19 H5 H1 0 0 0 1 1 0.000061 0.000000 + 20 C6 CT 6 0 0 1 1 0.194970 0.000000 + 212H6 H1 0 0 0 1 1 -0.034709 0.000000 + 223H6 H1 0 0 0 1 1 -0.034709 0.000000 + 23 OR OS 0 0 0 1 1 -0.456655 0.000000 + 1 2 + 1 3 + 1 23 + 3 4 + 3 5 + 3 9 + 5 6 + 5 7 + 7 8 + 9 10 + 9 11 + 9 14 + 11 12 + 12 13 + 14 15 + 14 16 + 14 18 + 16 17 + 18 19 + 18 20 + 18 23 + 20 21 + 20 22 diff --git a/src/data/amber_q/lps_ec/GN2.frg b/src/data/amber_q/lps_ec/GN2.frg new file mode 100644 index 0000000000..7d5a4543f9 --- /dev/null +++ b/src/data/amber_q/lps_ec/GN2.frg @@ -0,0 +1,53 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 09:21:31 +# +$GN2 + 22 1 1 0 +GN2 + 1 C1 AC 0 0 0 1 1 0.867086 0.000000 + 2 H1 H2 0 0 0 1 1 0.027072 0.000000 + 3 O1 OS 3 0 0 1 1 -0.352386 0.000000 + 4 C2 CT 0 0 0 1 1 0.087392 0.000000 + 5 H2 H1 0 0 0 1 1 0.644627 0.000000 + 6 N N 0 1 0 1 1 -0.482697 0.000000 + 7 H H 0 0 0 1 1 0.245772 0.000000 + 8 C C 4 1 0 1 1 0.842243 0.000000 + 9 O O 0 0 0 1 1 -0.644087 0.000000 + 10 C3 CT 0 0 0 1 1 -0.566141 0.000000 + 11 H3 H1 0 0 0 1 1 0.436671 0.000000 + 12 O3 OS 0 0 0 1 1 -0.576950 0.000000 + 13 CO3 C 5 1 0 1 1 0.821854 0.000000 + 14 OO3 O 0 0 0 1 1 -0.653878 0.000000 + 15 C4 CT 6 0 0 1 1 -0.437006 0.000000 + 16 H4 H1 0 0 0 1 1 0.057250 0.000000 + 17 C5 CT 0 0 0 1 1 1.056769 0.000000 + 18 H5 H1 0 0 0 1 1 -0.185588 0.000000 + 19 C6 CT 7 0 0 1 1 -0.579400 0.000000 + 202H6 H1 0 0 0 1 1 0.127390 0.000000 + 213H6 H1 0 0 0 1 1 0.127390 0.000000 + 22 OR OS 0 0 0 1 1 -0.863384 0.000000 + 1 2 + 1 3 + 1 4 + 1 22 + 4 5 + 4 6 + 4 10 + 6 7 + 6 8 + 8 9 + 10 11 + 10 12 + 10 15 + 12 13 + 13 14 + 15 16 + 15 17 + 17 18 + 17 19 + 17 22 + 19 20 + 19 21 diff --git a/src/data/amber_q/lps_ec/HE1.frg b/src/data/amber_q/lps_ec/HE1.frg new file mode 100644 index 0000000000..47c53b71fa --- /dev/null +++ b/src/data/amber_q/lps_ec/HE1.frg @@ -0,0 +1,55 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 10:35:31 +# +$HE1 + 23 1 1 0 +HE1 + 1 C1 AC 0 0 0 1 1 0.592716 0.000000 + 2 H1 H2 0 0 0 1 1 0.127829 0.000000 + 3 O1 OS 3 0 0 1 1 -0.173746 0.000000 + 4 C2 CT 0 0 0 1 1 0.232872 0.000000 + 5 H2 H1 0 0 0 1 1 0.131111 0.000000 + 6 O2 OH 0 0 0 1 1 -0.641843 0.000000 + 7 HO2 HO 0 0 0 1 1 0.320002 0.000000 + 8 C3 CT 4 0 0 1 1 -0.228802 0.000000 + 9 H3 H1 0 0 0 1 1 0.132071 0.000000 + 10 C4 CT 5 0 0 1 1 -0.208550 0.000000 + 11 H4 H1 0 0 0 1 1 0.037906 0.000000 + 12 C5 CT 0 0 0 1 1 0.604080 0.000000 + 13 H5 H1 0 0 0 1 1 0.024648 0.000000 + 14 C6 CT 0 0 0 1 1 0.382943 0.000000 + 15 H6 H1 0 0 0 1 1 -0.005643 0.000000 + 16 O6 OH 0 0 0 1 1 -0.767993 0.000000 + 17 HO6 HO 0 0 0 1 1 0.474382 0.000000 + 18 C7 CT 0 0 0 1 1 0.192162 0.000000 + 192H7 H1 0 0 0 1 1 0.030341 0.000000 + 203H7 H1 0 0 0 1 1 0.030341 0.000000 + 21 O7 OH 0 0 0 1 1 -0.730966 0.000000 + 22 HO7 HO 0 0 0 1 1 0.397321 0.000000 + 23 OR OS 0 0 0 1 1 -0.953182 0.000000 + 1 2 + 1 3 + 1 4 + 1 23 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 10 11 + 10 12 + 12 13 + 12 14 + 12 23 + 14 15 + 14 16 + 14 18 + 16 17 + 18 19 + 18 20 + 18 21 + 21 22 diff --git a/src/data/amber_q/lps_ec/HE2.frg b/src/data/amber_q/lps_ec/HE2.frg new file mode 100644 index 0000000000..ea2906f7dd --- /dev/null +++ b/src/data/amber_q/lps_ec/HE2.frg @@ -0,0 +1,51 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 10:35:31 +# +$HE2 + 21 1 1 0 +HE2 + 1 C1 AC 0 0 0 1 1 0.055732 0.000000 + 2 H1 H2 0 0 0 1 1 0.297481 0.000000 + 3 O1 OS 3 0 0 1 1 -0.009603 0.000000 + 4 C2 CT 0 0 0 1 1 0.486124 0.000000 + 5 H2 H1 0 0 0 1 1 0.052431 0.000000 + 6 O2 OH 0 0 0 1 1 -1.072662 0.000000 + 7 HO2 HO 0 0 0 1 1 0.424104 0.000000 + 8 C3 CT 4 0 0 1 1 -0.150164 0.000000 + 9 H3 H1 0 0 0 1 1 0.107220 0.000000 + 10 C4 CT 5 0 0 1 1 -0.202032 0.000000 + 11 H4 H1 0 0 0 1 1 0.010899 0.000000 + 12 C5 CT 0 0 0 1 1 0.499131 0.000000 + 13 H5 H1 0 0 0 1 1 0.004472 0.000000 + 14 C6 CT 0 0 0 1 1 0.438346 0.000000 + 15 H6 H1 0 0 0 1 1 0.094474 0.000000 + 16 O6 OH 0 0 0 1 1 -0.956445 0.000000 + 17 HO6 HO 0 0 0 1 1 0.658432 0.000000 + 18 C7 CT 6 0 0 1 1 -0.313208 0.000000 + 192H7 H1 0 0 0 1 1 0.071185 0.000000 + 203H7 H1 0 0 0 1 1 0.071185 0.000000 + 21 OR OS 0 0 0 1 1 -0.567101 0.000000 + 1 2 + 1 3 + 1 4 + 1 21 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 10 11 + 10 12 + 12 13 + 12 14 + 12 21 + 14 15 + 14 16 + 14 18 + 16 17 + 18 19 + 18 20 diff --git a/src/data/amber_q/lps_ec/HE3.frg b/src/data/amber_q/lps_ec/HE3.frg new file mode 100644 index 0000000000..88b156a94d --- /dev/null +++ b/src/data/amber_q/lps_ec/HE3.frg @@ -0,0 +1,63 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 10:35:31 +# +$HE3 + 27 1 1 0 +HE3 + 1 C1 AC 0 0 0 1 1 0.233788 0.000000 + 2 H1 H2 0 0 0 1 1 0.115911 0.000000 + 3 O1 OS 3 0 0 1 1 -0.065698 0.000000 + 4 C2 CT 0 0 0 1 1 0.293831 0.000000 + 5 H2 H1 0 0 0 1 1 0.096511 0.000000 + 6 O2 OH 0 0 0 1 1 -0.802055 0.000000 + 7 HO2 HO 0 0 0 1 1 0.423832 0.000000 + 8 C3 CT 0 0 0 1 1 0.529912 0.000000 + 9 H3 H1 0 0 0 1 1 0.093653 0.000000 + 10 O3 OH 0 0 0 1 1 -1.174772 0.000000 + 11 HO3 HO 0 0 0 1 1 0.552521 0.000000 + 12 C4 CT 0 0 0 1 1 0.394630 0.000000 + 13 H4 H1 0 0 0 1 1 0.096111 0.000000 + 14 O4 OH 0 0 0 1 1 -0.771900 0.000000 + 15 HO4 HO 0 0 0 1 1 0.416045 0.000000 + 16 C5 CT 0 0 0 1 1 0.137365 0.000000 + 17 H5 H1 0 0 0 1 1 -0.086477 0.000000 + 18 C6 CT 0 0 0 1 1 0.625346 0.000000 + 19 H6 H1 0 0 0 1 1 -0.050535 0.000000 + 20 O6 OH 0 0 0 1 1 -0.839967 0.000000 + 21 HO6 HO 0 0 0 1 1 0.458187 0.000000 + 22 C7 CT 0 0 0 1 1 0.264072 0.000000 + 232H7 H1 0 0 0 1 1 0.001987 0.000000 + 243H7 H1 0 0 0 1 1 0.001987 0.000000 + 25 O7 OH 0 0 0 1 1 -0.798300 0.000000 + 26 HO7 HO 0 0 0 1 1 0.466929 0.000000 + 27 OR OS 0 0 0 1 1 -0.612914 0.000000 + 1 2 + 1 3 + 1 4 + 1 27 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 + 8 12 + 10 11 + 12 13 + 12 14 + 12 16 + 14 15 + 16 17 + 16 18 + 16 27 + 18 19 + 18 20 + 18 22 + 20 21 + 22 23 + 22 24 + 22 25 + 25 26 diff --git a/src/data/amber_q/lps_ec/HE4.frg b/src/data/amber_q/lps_ec/HE4.frg new file mode 100644 index 0000000000..297681f1da --- /dev/null +++ b/src/data/amber_q/lps_ec/HE4.frg @@ -0,0 +1,63 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 10:35:31 +# +$HE4 + 27 1 1 0 +HE4 + 1 C1 AC 0 0 0 1 1 0.543249 0.000000 + 2 H1 H2 0 0 0 1 1 0.053887 0.000000 + 3 O1 OS 3 0 0 1 1 -0.289124 0.000000 + 4 C2 CT 0 0 0 1 1 0.207822 0.000000 + 5 H2 H1 0 0 0 1 1 0.074666 0.000000 + 6 O2 OH 0 0 0 1 1 -0.814166 0.000000 + 7 HO2 HO 0 0 0 1 1 0.490041 0.000000 + 8 C3 CT 0 0 0 1 1 0.578052 0.000000 + 9 H3 H1 0 0 0 1 1 -0.059410 0.000000 + 10 O3 OH 0 0 0 1 1 -0.827632 0.000000 + 11 HO3 HO 0 0 0 1 1 0.468295 0.000000 + 12 C4 CT 0 0 0 1 1 0.014820 0.000000 + 13 H4 H1 0 0 0 1 1 0.072476 0.000000 + 14 O4 OH 0 0 0 1 1 -0.741547 0.000000 + 15 HO4 HO 0 0 0 1 1 0.436432 0.000000 + 16 C5 CT 0 0 0 1 1 0.397046 0.000000 + 17 H5 H1 0 0 0 1 1 0.048543 0.000000 + 18 C6 CT 0 0 0 1 1 0.261450 0.000000 + 19 H6 H1 0 0 0 1 1 -0.001659 0.000000 + 20 O6 OH 0 0 0 1 1 -0.726431 0.000000 + 21 HO6 HO 0 0 0 1 1 0.435584 0.000000 + 22 C7 CT 0 0 0 1 1 0.323405 0.000000 + 232H7 H1 0 0 0 1 1 0.003574 0.000000 + 243H7 H1 0 0 0 1 1 0.003574 0.000000 + 25 O7 OH 0 0 0 1 1 -0.723675 0.000000 + 26 HO7 HO 0 0 0 1 1 0.449974 0.000000 + 27 OR OS 0 0 0 1 1 -0.679246 0.000000 + 1 2 + 1 3 + 1 4 + 1 27 + 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 + 16 27 + 18 19 + 18 20 + 18 22 + 20 21 + 22 23 + 22 24 + 22 25 + 25 26 diff --git a/src/data/amber_q/lps_ec/KD1.frg b/src/data/amber_q/lps_ec/KD1.frg new file mode 100644 index 0000000000..66707e5170 --- /dev/null +++ b/src/data/amber_q/lps_ec/KD1.frg @@ -0,0 +1,57 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 10:35:31 +# +$KD1 + 24 1 1 0 +KD1 + 1 C1 C 0 1 0 1 1 1.609759 0.000000 + 2 O11 O2 0 0 0 1 1 -1.420645 0.000000 + 3 O12 O2 0 0 0 1 1 -1.095936 0.000000 + 4 C2 AC 0 0 0 1 1 0.316410 0.000000 + 5 O2 OS 3 0 0 1 1 -0.089481 0.000000 + 6 C3 CT 0 0 0 1 1 -0.039435 0.000000 + 72H3 HC 0 0 0 1 1 0.041299 0.000000 + 83H3 HC 0 0 0 1 1 0.041299 0.000000 + 9 C4 CT 4 0 0 1 1 -0.133820 0.000000 + 10 H4 H1 0 0 0 1 1 0.154209 0.000000 + 11 C5 CT 5 0 0 1 1 -0.306006 0.000000 + 12 H5 H1 0 0 0 1 1 0.234593 0.000000 + 13 C6 CT 0 0 0 1 1 0.294750 0.000000 + 14 H6 H1 0 0 0 1 1 0.034444 0.000000 + 15 C7 CT 0 0 0 1 1 0.090478 0.000000 + 16 H7 H1 0 0 0 1 1 0.091281 0.000000 + 17 O7 OH 0 0 0 1 1 -0.740663 0.000000 + 18 HO7 HO 0 0 0 1 1 0.425276 0.000000 + 19 C8 CT 0 0 0 1 1 0.648942 0.000000 + 202H8 H1 0 0 0 1 1 -0.110336 0.000000 + 213H8 H1 0 0 0 1 1 -0.110336 0.000000 + 22 O8 OH 0 0 0 1 1 -0.840923 0.000000 + 23 HO8 HO 0 0 0 1 1 0.462830 0.000000 + 24 OR OS 0 0 0 1 1 -0.557987 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 4 6 + 4 24 + 6 7 + 6 8 + 6 9 + 9 10 + 9 11 + 11 12 + 11 13 + 13 14 + 13 15 + 13 24 + 15 16 + 15 17 + 15 19 + 17 18 + 19 20 + 19 21 + 19 22 + 22 23 diff --git a/src/data/amber_q/lps_ec/KD2.frg b/src/data/amber_q/lps_ec/KD2.frg new file mode 100644 index 0000000000..8c6182251b --- /dev/null +++ b/src/data/amber_q/lps_ec/KD2.frg @@ -0,0 +1,65 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 10:35:31 +# +$KD2 + 28 1 1 0 +KD2 + 1 C1 C 0 1 0 1 1 1.194884 0.000000 + 2 O11 O2 0 0 0 1 1 -1.006920 0.000000 + 3 O12 O2 0 0 0 1 1 -1.032685 0.000000 + 4 C2 AC 0 0 0 1 1 0.247898 0.000000 + 5 O2 OS 3 0 0 1 1 -0.169823 0.000000 + 6 C3 CT 0 0 0 1 1 -0.112596 0.000000 + 72H3 HC 0 0 0 1 1 0.029839 0.000000 + 83H3 HC 0 0 0 1 1 0.029839 0.000000 + 9 C4 CT 0 0 0 1 1 0.398654 0.000000 + 10 H4 H1 0 0 0 1 1 -0.021858 0.000000 + 11 O4 OH 0 0 0 1 1 -0.812111 0.000000 + 12 HO4 HO 0 0 0 1 1 0.469651 0.000000 + 13 C5 CT 0 0 0 1 1 0.444025 0.000000 + 14 H5 H1 0 0 0 1 1 -0.039673 0.000000 + 15 O5 OH 0 0 0 1 1 -0.806948 0.000000 + 16 HO5 HO 0 0 0 1 1 0.460309 0.000000 + 17 C6 CT 0 0 0 1 1 0.214383 0.000000 + 18 H6 H1 0 0 0 1 1 0.052915 0.000000 + 19 C7 CT 0 0 0 1 1 0.404323 0.000000 + 20 H7 H1 0 0 0 1 1 0.015334 0.000000 + 21 O7 OH 0 0 0 1 1 -0.891275 0.000000 + 22 HO7 HO 0 0 0 1 1 0.507523 0.000000 + 23 C8 CT 0 0 0 1 1 0.152401 0.000000 + 242H8 H1 0 0 0 1 1 0.030152 0.000000 + 253H8 H1 0 0 0 1 1 0.030152 0.000000 + 26 O8 OH 0 0 0 1 1 -0.701123 0.000000 + 27 HO8 HO 0 0 0 1 1 0.451598 0.000000 + 28 OR OS 0 0 0 1 1 -0.538866 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 4 6 + 4 28 + 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 + 17 28 + 19 20 + 19 21 + 19 23 + 21 22 + 23 24 + 23 25 + 23 26 + 26 27 diff --git a/src/data/amber_q/lps_ec/PO4.frg b/src/data/amber_q/lps_ec/PO4.frg new file mode 100644 index 0000000000..e3649746d3 --- /dev/null +++ b/src/data/amber_q/lps_ec/PO4.frg @@ -0,0 +1,18 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 09:21:31 +# +$PO4 + 5 1 1 0 +PO4 + 1 OP1 OS 3 0 0 1 1 -0.139474 0.000000 + 2 P P 0 0 0 1 1 0.938933 0.000000 + 3 OP2 O2 0 0 0 1 1 -0.933153 0.000000 + 4 OP3 O2 0 0 0 1 1 -0.933153 0.000000 + 5 OP4 O2 0 0 0 1 1 -0.933153 0.000000 + 1 2 + 2 3 + 2 4 + 2 5 diff --git a/src/data/amber_q/lps_ec/POC.frg b/src/data/amber_q/lps_ec/POC.frg new file mode 100644 index 0000000000..71e9a5c9cb --- /dev/null +++ b/src/data/amber_q/lps_ec/POC.frg @@ -0,0 +1,35 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude estimates +# 08/24/05 11:36:33 +# +$POC + 14 1 1 0 +POC + 1 C1 CT 3 0 0 1 1 -0.104211 0.000000 + 22H1 HC 0 0 0 1 1 0.010288 0.000000 + 33H1 HC 0 0 0 1 1 0.010288 0.000000 + 4 C2 CT 0 0 0 1 1 0.330088 0.000000 + 5 H2 H1 0 0 0 1 1 -0.000292 0.000000 + 6 O2 OS 0 0 0 1 1 -0.633243 0.000000 + 7 C3 CT 4 0 0 1 1 0.016752 0.000000 + 82H3 HC 0 0 0 1 1 0.001054 0.000000 + 93H3 HC 0 0 0 1 1 0.001054 0.000000 + 10 C4 C 0 1 0 1 1 0.782302 0.000000 + 11 O4 O 0 0 0 1 1 -0.540273 0.000000 + 12 C5 CT 5 0 0 1 1 -0.017987 0.000000 + 132H5 HC 0 0 0 1 1 0.072090 0.000000 + 143H5 HC 0 0 0 1 1 0.072090 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 4 6 + 4 7 + 6 10 + 7 8 + 7 9 + 10 11 + 10 12 + 12 13 + 12 14 diff --git a/src/data/amber_q/lps_ec/POH.frg b/src/data/amber_q/lps_ec/POH.frg new file mode 100644 index 0000000000..dbdd0f0289 --- /dev/null +++ b/src/data/amber_q/lps_ec/POH.frg @@ -0,0 +1,28 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 09:21:31 +# +$POH + 10 1 1 0 +POH + 1 C1 CT 3 0 0 1 1 0.341188 0.000000 + 22H1 HC 0 0 0 1 1 -0.101849 0.000000 + 33H1 HC 0 0 0 1 1 -0.101849 0.000000 + 4 C2 CT 0 0 0 1 1 0.432090 0.000000 + 5 H2 H1 0 0 0 1 1 0.030800 0.000000 + 6 O2 OH 0 0 0 1 1 -0.860879 0.000000 + 7 HO2 HO 0 0 0 1 1 0.450697 0.000000 + 8 C3 CT 4 0 0 1 1 -0.583445 0.000000 + 92H3 HC 0 0 0 1 1 0.196624 0.000000 + 103H3 HC 0 0 0 1 1 0.196624 0.000000 + 1 2 + 1 3 + 1 4 + 4 5 + 4 6 + 4 8 + 6 7 + 8 9 + 8 10 diff --git a/src/data/amber_q/lps_ec/PT1.frg b/src/data/amber_q/lps_ec/PT1.frg new file mode 100644 index 0000000000..b2db1a7bfd --- /dev/null +++ b/src/data/amber_q/lps_ec/PT1.frg @@ -0,0 +1,40 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 09:21:31 +# +$PT1 + 16 1 1 0 +PT1 + 1 C1 CT 3 0 0 1 1 0.195684 0.000000 + 22H1 HC 0 0 0 1 1 -0.062894 0.000000 + 33H1 HC 0 0 0 1 1 -0.062894 0.000000 + 4 C2 CT 0 0 0 1 1 0.011013 0.000000 + 52H2 HC 0 0 0 1 1 0.029913 0.000000 + 63H2 HC 0 0 0 1 1 0.029913 0.000000 + 7 C3 CT 0 0 0 1 1 -0.682627 0.000000 + 82H3 HC 0 0 0 1 1 0.218569 0.000000 + 93H3 HC 0 0 0 1 1 0.218569 0.000000 + 10 C4 CT 0 0 0 1 1 0.107450 0.000000 + 112H4 HC 0 0 0 1 1 0.035748 0.000000 + 123H4 HC 0 0 0 1 1 0.035748 0.000000 + 13 C5 CT 0 0 0 1 1 -0.030578 0.000000 + 142H5 HC 0 0 0 1 1 -0.014538 0.000000 + 153H5 HC 0 0 0 1 1 -0.014538 0.000000 + 164H5 HC 0 0 0 1 1 -0.014538 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/lps_ec/PT2.frg b/src/data/amber_q/lps_ec/PT2.frg new file mode 100644 index 0000000000..f97d6c3125 --- /dev/null +++ b/src/data/amber_q/lps_ec/PT2.frg @@ -0,0 +1,38 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges determined from a three-stage RESP fit +# for the Rough LPS of e coli with counter ions +# 07/14/06 09:21:31 +# +$PT2 + 15 1 1 0 +PT2 + 1 C1 CT 3 0 0 1 1 -0.241902 0.000000 + 22H1 HC 0 0 0 1 1 0.025797 0.000000 + 33H1 HC 0 0 0 1 1 0.025797 0.000000 + 4 C2 CT 0 0 0 1 1 0.484331 0.000000 + 52H2 HC 0 0 0 1 1 -0.132786 0.000000 + 63H2 HC 0 0 0 1 1 -0.132786 0.000000 + 7 C3 CT 0 0 0 1 1 0.606360 0.000000 + 82H3 HC 0 0 0 1 1 -0.018041 0.000000 + 93H3 HC 0 0 0 1 1 -0.018041 0.000000 + 10 C4 CT 0 0 0 1 1 -0.077118 0.000000 + 112H4 HC 0 0 0 1 1 0.047634 0.000000 + 123H4 HC 0 0 0 1 1 0.047634 0.000000 + 13 C5 CT 4 0 0 1 1 -0.095495 0.000000 + 142H5 HC 0 0 0 1 1 0.012170 0.000000 + 153H5 HC 0 0 0 1 1 0.012170 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