diff --git a/src/data/amber_s/HSE.frg b/src/data/amber_s/HSE.frg new file mode 100644 index 0000000000..2038b71162 --- /dev/null +++ b/src/data/amber_s/HSE.frg @@ -0,0 +1,40 @@ +# This is an automatically generated fragment file +# Atom types and connectivity were derived from coordinates +# Atomic partial charges are crude estimates +$HSE + 17 1 1 0 +HSE + 1 N N 1 1 0 1 1 -0.340000 0.000000 + 2 HN H 0 0 0 1 1 0.270000 0.000000 + 3 CA CT 0 0 0 1 1 0.020000 0.000000 + 4 HA H1 0 0 0 1 1 0.050000 0.000000 + 5 NE2 NA 0 5 0 1 1 -0.410000 0.000000 + 6 HE2 H 0 0 0 1 1 0.270000 0.000000 + 7 CD2 CW 0 5 0 1 1 0.020000 0.000000 + 8 HD2 H4 0 0 0 1 1 0.050000 0.000000 + 9 ND1 NB 0 5 0 1 1 -0.140000 0.000000 + 10 CG CC 0 5 0 1 1 0.070000 0.000000 + 11 CE1 CR 0 5 0 1 1 0.090000 0.000000 + 12 HE1 H5 0 0 0 1 1 0.050000 0.000000 + 13 CB CT 0 0 0 1 1 -0.100000 0.000000 + 14 HB1 HC 0 0 0 1 1 0.050000 0.000000 + 15 HB2 HC 0 0 0 1 1 0.050000 0.000000 + 16 C C 4 1 0 1 1 0.570000 0.000000 + 17 O O 0 0 0 1 1 -0.570000 0.000000 + 1 2 + 1 3 + 3 4 + 3 13 + 3 16 + 5 6 + 5 7 + 5 11 + 7 8 + 7 10 + 9 10 + 9 11 + 10 13 + 11 12 + 13 14 + 13 15 + 16 17 diff --git a/src/data/charmm_s/ALA.frg b/src/data/charmm_s/ALA.frg index f636c76348..d545cd4da1 100644 --- a/src/data/charmm_s/ALA.frg +++ b/src/data/charmm_s/ALA.frg @@ -1,5 +1,6 @@ $ALA - 10 + 10 1 1 0 +ALA 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/ALA_C.frg b/src/data/charmm_s/ALA_C.frg index c9661999de..5dfa75b0e5 100644 --- a/src/data/charmm_s/ALA_C.frg +++ b/src/data/charmm_s/ALA_C.frg @@ -1,5 +1,6 @@ $ALA_C - 11 + 11 1 1 0 +ALA_C 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/ALA_N.frg b/src/data/charmm_s/ALA_N.frg index 7e5d294210..3a031330ac 100644 --- a/src/data/charmm_s/ALA_N.frg +++ b/src/data/charmm_s/ALA_N.frg @@ -1,5 +1,6 @@ $ALA_N - 12 + 12 1 1 0 +ALA_N 1 N NH3 0 0 1 1 -0.300000 0.000000 22H HC 0 0 1 1 0.330000 0.000000 33H HC 0 0 1 1 0.330000 0.000000 diff --git a/src/data/charmm_s/ARG.frg b/src/data/charmm_s/ARG.frg index 8baae89670..37f2bcfa34 100644 --- a/src/data/charmm_s/ARG.frg +++ b/src/data/charmm_s/ARG.frg @@ -1,5 +1,6 @@ $ARG - 24 + 24 1 1 0 +ARG 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/ARG_C.frg b/src/data/charmm_s/ARG_C.frg index 21bb6b03ef..26a8825ad6 100644 --- a/src/data/charmm_s/ARG_C.frg +++ b/src/data/charmm_s/ARG_C.frg @@ -1,5 +1,6 @@ $ARG_C - 25 + 25 1 1 0 +ARG_C 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/ARG_N.frg b/src/data/charmm_s/ARG_N.frg index 1928d35ca2..86b66c500a 100644 --- a/src/data/charmm_s/ARG_N.frg +++ b/src/data/charmm_s/ARG_N.frg @@ -1,5 +1,6 @@ $ARG_N - 26 + 26 1 1 0 +ARG_N 1 N NH3 0 0 1 1 -0.300000 0.000000 22H HC 0 0 1 1 0.330000 0.000000 33H HC 0 0 1 1 0.330000 0.000000 diff --git a/src/data/charmm_s/ASN.frg b/src/data/charmm_s/ASN.frg index 9ba8be6ce7..1e6d763a14 100644 --- a/src/data/charmm_s/ASN.frg +++ b/src/data/charmm_s/ASN.frg @@ -1,5 +1,6 @@ $ASN - 14 + 14 1 1 0 +ASN 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/ASN_C.frg b/src/data/charmm_s/ASN_C.frg index 5814d57e25..63674762e4 100644 --- a/src/data/charmm_s/ASN_C.frg +++ b/src/data/charmm_s/ASN_C.frg @@ -1,5 +1,6 @@ $ASN_C - 15 + 15 1 1 0 +ASN_C 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/ASN_N.frg b/src/data/charmm_s/ASN_N.frg index 52ad115f84..640756c5f9 100644 --- a/src/data/charmm_s/ASN_N.frg +++ b/src/data/charmm_s/ASN_N.frg @@ -1,5 +1,6 @@ $ASN_N - 16 + 16 1 1 0 +ASN_N 1 N NH3 0 0 1 1 -0.300000 0.000000 22H HC 0 0 1 1 0.330000 0.000000 33H HC 0 0 1 1 0.330000 0.000000 diff --git a/src/data/charmm_s/ASP.frg b/src/data/charmm_s/ASP.frg index a7608a5ae7..d5714b5cb8 100644 --- a/src/data/charmm_s/ASP.frg +++ b/src/data/charmm_s/ASP.frg @@ -1,5 +1,6 @@ $ASP - 12 + 12 1 1 0 +ASP 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/ASP_C.frg b/src/data/charmm_s/ASP_C.frg index 2af02a54d0..708a39bbb0 100644 --- a/src/data/charmm_s/ASP_C.frg +++ b/src/data/charmm_s/ASP_C.frg @@ -1,5 +1,6 @@ $ASP_C - 13 + 13 1 1 0 +ASP_C 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/ASP_N.frg b/src/data/charmm_s/ASP_N.frg index d934391ba5..b05b534e20 100644 --- a/src/data/charmm_s/ASP_N.frg +++ b/src/data/charmm_s/ASP_N.frg @@ -1,5 +1,6 @@ $ASP_N - 14 + 14 1 1 0 +ASP_N 1 N NH3 0 0 1 1 -0.300000 0.000000 22H HC 0 0 1 1 0.330000 0.000000 33H HC 0 0 1 1 0.330000 0.000000 diff --git a/src/data/charmm_s/CO.frg b/src/data/charmm_s/CO.frg index b4e00a1529..41cf17b20e 100644 --- a/src/data/charmm_s/CO.frg +++ b/src/data/charmm_s/CO.frg @@ -1,4 +1,5 @@ $CO - 2 + 2 1 1 0 +CO 1 C CM 0 0 1 1 0.020000 0.000000 2 O OM 0 0 1 1 -0.020000 0.000000 diff --git a/src/data/charmm_s/CYS.frg b/src/data/charmm_s/CYS.frg index 45926f3bc3..3c93e69463 100644 --- a/src/data/charmm_s/CYS.frg +++ b/src/data/charmm_s/CYS.frg @@ -1,5 +1,6 @@ -$CYSH - 11 +$CYS + 11 1 1 0 +CYS 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/CYS_C.frg b/src/data/charmm_s/CYS_C.frg index 98841eb569..706c895e07 100644 --- a/src/data/charmm_s/CYS_C.frg +++ b/src/data/charmm_s/CYS_C.frg @@ -1,5 +1,6 @@ $CYSH_C - 12 + 12 1 1 0 +CYSH_C 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/CYS_N.frg b/src/data/charmm_s/CYS_N.frg index 8ea2418f82..6cbd88d558 100644 --- a/src/data/charmm_s/CYS_N.frg +++ b/src/data/charmm_s/CYS_N.frg @@ -1,5 +1,6 @@ $CYSH_N - 13 + 13 1 1 0 +CYSH_N 1 N NH3 0 0 1 1 -0.300000 0.000000 22H HC 0 0 1 1 0.330000 0.000000 33H HC 0 0 1 1 0.330000 0.000000 diff --git a/src/data/charmm_s/CYX.frg b/src/data/charmm_s/CYX.frg index 70fdb04d6b..917a02b791 100644 --- a/src/data/charmm_s/CYX.frg +++ b/src/data/charmm_s/CYX.frg @@ -1,5 +1,6 @@ -$CYS - 10 +$CYX + 10 1 1 0 +CYX 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 @@ -7,7 +8,7 @@ $CYS 5 CB CT2 0 0 2 1 -0.100000 0.000000 62HB HA 0 0 2 1 0.090000 0.000000 73HB HA 0 0 2 1 0.090000 0.000000 - 8 SG S 3 0 2 1 -0.080000 0.000000 + 8 SG SM 3 0 2 1 -0.080000 0.000000 9 C C 2 1 3 1 0.510000 0.000000 10 O O 0 0 3 1 -0.510000 0.000000 1 2 diff --git a/src/data/charmm_s/CYX_C.frg b/src/data/charmm_s/CYX_C.frg index e01ce1ed1f..0e10d102d2 100644 --- a/src/data/charmm_s/CYX_C.frg +++ b/src/data/charmm_s/CYX_C.frg @@ -1,5 +1,6 @@ $CYS_C - 11 + 11 1 1 0 +CYS_C 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/CYX_N.frg b/src/data/charmm_s/CYX_N.frg index 8862852c7d..d0c7321006 100644 --- a/src/data/charmm_s/CYX_N.frg +++ b/src/data/charmm_s/CYX_N.frg @@ -1,5 +1,6 @@ $CYS_N - 12 + 12 1 1 0 +CYS_N 1 N NH3 0 0 1 1 -0.300000 0.000000 22H HC 0 0 1 1 0.330000 0.000000 33H HC 0 0 1 1 0.330000 0.000000 diff --git a/src/data/charmm_s/DUM.frg b/src/data/charmm_s/DUM.frg index 9ab3a69143..c12cc9c571 100644 --- a/src/data/charmm_s/DUM.frg +++ b/src/data/charmm_s/DUM.frg @@ -1,3 +1,4 @@ $DUM - 1 + 1 1 1 0 +DUM 1 DUM DUM 0 0 1 1 0.000000 0.000000 diff --git a/src/data/charmm_s/GLN.frg b/src/data/charmm_s/GLN.frg index f93ec6576c..9913e48eb2 100644 --- a/src/data/charmm_s/GLN.frg +++ b/src/data/charmm_s/GLN.frg @@ -1,5 +1,6 @@ $GLN - 17 + 17 1 1 0 +GLN 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/GLN_C.frg b/src/data/charmm_s/GLN_C.frg index 1965edcd49..77104611b6 100644 --- a/src/data/charmm_s/GLN_C.frg +++ b/src/data/charmm_s/GLN_C.frg @@ -1,5 +1,6 @@ $GLN_C - 19 + 19 1 1 0 +GLN_C 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/GLN_N.frg b/src/data/charmm_s/GLN_N.frg index 777b7f8966..d6f5a271f9 100644 --- a/src/data/charmm_s/GLN_N.frg +++ b/src/data/charmm_s/GLN_N.frg @@ -1,5 +1,6 @@ $GLN_N - 19 + 19 1 1 0 +GLN_N 1 N NH3 0 0 1 1 -0.300000 0.000000 22H HC 0 0 1 1 0.330000 0.000000 33H HC 0 0 1 1 0.330000 0.000000 diff --git a/src/data/charmm_s/GLU.frg b/src/data/charmm_s/GLU.frg index 8c6660beec..17ff81b319 100644 --- a/src/data/charmm_s/GLU.frg +++ b/src/data/charmm_s/GLU.frg @@ -1,5 +1,6 @@ $GLU - 15 + 15 1 1 0 +GLU 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/GLU_C.frg b/src/data/charmm_s/GLU_C.frg index d8ccf67207..006bfeab13 100644 --- a/src/data/charmm_s/GLU_C.frg +++ b/src/data/charmm_s/GLU_C.frg @@ -1,5 +1,6 @@ $GLU_C - 16 + 16 1 1 0 +GLU_C 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/GLU_N.frg b/src/data/charmm_s/GLU_N.frg index db3db12816..e486911e8d 100644 --- a/src/data/charmm_s/GLU_N.frg +++ b/src/data/charmm_s/GLU_N.frg @@ -1,5 +1,6 @@ $GLU_N - 17 + 17 1 1 0 +GLU_N 1 N NH3 0 0 1 1 -0.300000 0.000000 22H HC 0 0 1 1 0.330000 0.000000 33H HC 0 0 1 1 0.330000 0.000000 diff --git a/src/data/charmm_s/GLY.frg b/src/data/charmm_s/GLY.frg index db0313b56c..fddf3b90ae 100644 --- a/src/data/charmm_s/GLY.frg +++ b/src/data/charmm_s/GLY.frg @@ -1,5 +1,6 @@ $GLY - 7 + 7 1 1 0 +GLY 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT2 0 0 1 1 -0.020000 0.000000 diff --git a/src/data/charmm_s/GLY_C.frg b/src/data/charmm_s/GLY_C.frg index e04c681f56..c4bac3f8c8 100644 --- a/src/data/charmm_s/GLY_C.frg +++ b/src/data/charmm_s/GLY_C.frg @@ -1,5 +1,6 @@ $GLY_C - 8 + 8 1 1 0 +GLY_C 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT2 0 0 1 1 -0.020000 0.000000 diff --git a/src/data/charmm_s/GLY_N.frg b/src/data/charmm_s/GLY_N.frg index 06ffa033fc..14d8eeb051 100644 --- a/src/data/charmm_s/GLY_N.frg +++ b/src/data/charmm_s/GLY_N.frg @@ -1,5 +1,6 @@ $GLY_N - 9 + 9 1 1 0 +GLY_N 1 N NH3 0 0 1 1 -0.300000 0.000000 22H HC 0 0 1 1 0.330000 0.000000 33H HC 0 0 1 1 0.330000 0.000000 diff --git a/src/data/charmm_s/HEME.frg b/src/data/charmm_s/HEME.frg index 16ede487ec..9c0b5558d1 100644 --- a/src/data/charmm_s/HEME.frg +++ b/src/data/charmm_s/HEME.frg @@ -1,5 +1,6 @@ $HEME - 73 + 73 1 1 0 +HEME 1FE FE 0 0 1 1 0.240000 0.000000 2 NA NPH 0 1 1 1 -0.180000 0.000000 3 NB NPH 0 1 1 1 -0.180000 0.000000 diff --git a/src/data/charmm_s/HSD.frg b/src/data/charmm_s/HSD.frg index 3e685e6b35..f9f34aae62 100644 --- a/src/data/charmm_s/HSD.frg +++ b/src/data/charmm_s/HSD.frg @@ -1,5 +1,6 @@ $HSD - 17 + 17 1 1 0 +HSD 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/HSD_C.frg b/src/data/charmm_s/HSD_C.frg index a0d70b7571..b99045111f 100644 --- a/src/data/charmm_s/HSD_C.frg +++ b/src/data/charmm_s/HSD_C.frg @@ -1,5 +1,6 @@ $HSD_C - 18 + 18 1 1 0 +HSD_C 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/HSD_N.frg b/src/data/charmm_s/HSD_N.frg index 70c966837b..94ca2b3422 100644 --- a/src/data/charmm_s/HSD_N.frg +++ b/src/data/charmm_s/HSD_N.frg @@ -1,5 +1,6 @@ $HSD_N - 19 + 19 1 1 0 +HSD_N 1 N NH3 0 0 1 1 -0.300000 0.000000 22H HC 0 0 1 1 0.330000 0.000000 33H HC 0 0 1 1 0.330000 0.000000 diff --git a/src/data/charmm_s/HSE.frg b/src/data/charmm_s/HSE.frg index 2a1ec95f56..9842685446 100644 --- a/src/data/charmm_s/HSE.frg +++ b/src/data/charmm_s/HSE.frg @@ -1,5 +1,6 @@ $HSE - 17 + 17 1 1 0 +HSE 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/HSE_C.frg b/src/data/charmm_s/HSE_C.frg index e0467bb02a..812df194b2 100644 --- a/src/data/charmm_s/HSE_C.frg +++ b/src/data/charmm_s/HSE_C.frg @@ -1,5 +1,6 @@ $HSE_C - 18 + 18 1 1 0 +HSE_C 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/HSE_N.frg b/src/data/charmm_s/HSE_N.frg index f681110124..ff912053b8 100644 --- a/src/data/charmm_s/HSE_N.frg +++ b/src/data/charmm_s/HSE_N.frg @@ -1,5 +1,6 @@ $HSE_N - 19 + 19 1 1 0 +HSE_N 1 N NH3 0 0 1 1 -0.300000 0.000000 22H HC 0 0 1 1 0.330000 0.000000 33H HC 0 0 1 1 0.330000 0.000000 diff --git a/src/data/charmm_s/HSP.frg b/src/data/charmm_s/HSP.frg index bc5132c6ad..8bac3dca47 100644 --- a/src/data/charmm_s/HSP.frg +++ b/src/data/charmm_s/HSP.frg @@ -1,5 +1,6 @@ $HSP - 18 + 18 1 1 0 +HSP 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/HSP_C.frg b/src/data/charmm_s/HSP_C.frg index 08e12ec314..b0826ebf76 100644 --- a/src/data/charmm_s/HSP_C.frg +++ b/src/data/charmm_s/HSP_C.frg @@ -1,5 +1,6 @@ $HSP_C - 19 + 19 1 1 0 +HSP_C 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/HSP_N.frg b/src/data/charmm_s/HSP_N.frg index 343ef82428..654e50cac5 100644 --- a/src/data/charmm_s/HSP_N.frg +++ b/src/data/charmm_s/HSP_N.frg @@ -1,5 +1,6 @@ $HSP_N - 20 + 20 1 1 0 +HSP_N 1 N NH3 0 0 1 1 -0.300000 0.000000 22H HC 0 0 1 1 0.330000 0.000000 33H HC 0 0 1 1 0.330000 0.000000 diff --git a/src/data/charmm_s/ILE.frg b/src/data/charmm_s/ILE.frg index ec900fb5da..b9ba0ebd5b 100644 --- a/src/data/charmm_s/ILE.frg +++ b/src/data/charmm_s/ILE.frg @@ -1,5 +1,6 @@ $ILE - 19 + 19 1 1 0 +ILE 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/ILE_C.frg b/src/data/charmm_s/ILE_C.frg index 05ee1a69dc..94d6ce5d47 100644 --- a/src/data/charmm_s/ILE_C.frg +++ b/src/data/charmm_s/ILE_C.frg @@ -1,5 +1,6 @@ $ILE_C - 20 + 20 1 1 0 +ILE_C 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/ILE_N.frg b/src/data/charmm_s/ILE_N.frg index a44ef42adf..1306225301 100644 --- a/src/data/charmm_s/ILE_N.frg +++ b/src/data/charmm_s/ILE_N.frg @@ -1,5 +1,6 @@ $ILE_N - 21 + 21 1 1 0 +ILE_N 1 N NH3 0 0 1 1 -0.300000 0.000000 22H HC 0 0 1 1 0.330000 0.000000 33H HC 0 0 1 1 0.330000 0.000000 diff --git a/src/data/charmm_s/LEU.frg b/src/data/charmm_s/LEU.frg index 1967d407dc..68ccea11e8 100644 --- a/src/data/charmm_s/LEU.frg +++ b/src/data/charmm_s/LEU.frg @@ -1,5 +1,6 @@ $LEU - 19 + 19 1 1 0 +LEU 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/LEU_C.frg b/src/data/charmm_s/LEU_C.frg index 69a677f8d8..a571566080 100644 --- a/src/data/charmm_s/LEU_C.frg +++ b/src/data/charmm_s/LEU_C.frg @@ -1,5 +1,6 @@ $LEU_C - 20 + 20 1 1 0 +LEU_C 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/LEU_N.frg b/src/data/charmm_s/LEU_N.frg index 64b919d227..2a7bce0cb2 100644 --- a/src/data/charmm_s/LEU_N.frg +++ b/src/data/charmm_s/LEU_N.frg @@ -1,5 +1,6 @@ $LEU_N - 21 + 21 1 1 0 +LEU_N 1 N NH3 0 0 1 1 -0.300000 0.000000 22H HC 0 0 1 1 0.330000 0.000000 33H HC 0 0 1 1 0.330000 0.000000 diff --git a/src/data/charmm_s/LYS.frg b/src/data/charmm_s/LYS.frg index 012e9abae8..7cd76b8cdf 100644 --- a/src/data/charmm_s/LYS.frg +++ b/src/data/charmm_s/LYS.frg @@ -1,5 +1,6 @@ $LYS - 22 + 22 1 1 0 +LYS 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/LYS_C.frg b/src/data/charmm_s/LYS_C.frg index f2c1068f09..c0080870be 100644 --- a/src/data/charmm_s/LYS_C.frg +++ b/src/data/charmm_s/LYS_C.frg @@ -1,5 +1,6 @@ $LYS_C - 23 + 23 1 1 0 +LYS_C 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/LYS_N.frg b/src/data/charmm_s/LYS_N.frg index e8ee6890ac..2998d9da77 100644 --- a/src/data/charmm_s/LYS_N.frg +++ b/src/data/charmm_s/LYS_N.frg @@ -1,5 +1,6 @@ $LYS_N - 24 + 24 1 1 0 +LYS_N 1 N NH3 0 0 1 1 -0.300000 0.000000 22H HC 0 0 1 1 0.330000 0.000000 33H HC 0 0 1 1 0.330000 0.000000 diff --git a/src/data/charmm_s/MET.frg b/src/data/charmm_s/MET.frg index 845030f0d5..6083ac4785 100644 --- a/src/data/charmm_s/MET.frg +++ b/src/data/charmm_s/MET.frg @@ -1,5 +1,6 @@ $MET - 17 + 17 1 1 0 +MET 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/MET_C.frg b/src/data/charmm_s/MET_C.frg index 4b235140e5..8922a90c71 100644 --- a/src/data/charmm_s/MET_C.frg +++ b/src/data/charmm_s/MET_C.frg @@ -1,5 +1,6 @@ $MET_C - 18 + 18 1 1 0 +MET_C 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/MET_N.frg b/src/data/charmm_s/MET_N.frg index fa280c6ba2..f7c82b47fc 100644 --- a/src/data/charmm_s/MET_N.frg +++ b/src/data/charmm_s/MET_N.frg @@ -1,5 +1,6 @@ $MET_N - 19 + 19 1 1 0 +MET_N 1 N NH3 0 0 1 1 -0.300000 0.000000 22H HC 0 0 1 1 0.330000 0.000000 33H HC 0 0 1 1 0.330000 0.000000 diff --git a/src/data/charmm_s/O2.frg b/src/data/charmm_s/O2.frg index 9f8cfe67d3..42732ca9bd 100644 --- a/src/data/charmm_s/O2.frg +++ b/src/data/charmm_s/O2.frg @@ -1,5 +1,6 @@ $O2 - 2 + 2 1 1 0 +O2 1 O1 OM 0 0 1 1 0.020000 0.000000 2 O2 OM 0 0 1 1 -0.020000 0.000000 1 2 diff --git a/src/data/charmm_s/PHE.frg b/src/data/charmm_s/PHE.frg index 03a2a564cd..c7b1fb7f7e 100644 --- a/src/data/charmm_s/PHE.frg +++ b/src/data/charmm_s/PHE.frg @@ -1,5 +1,6 @@ $PHE - 20 + 20 1 1 0 +PHE 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/PHE_C.frg b/src/data/charmm_s/PHE_C.frg index 77b6710c27..71d1b2ad85 100644 --- a/src/data/charmm_s/PHE_C.frg +++ b/src/data/charmm_s/PHE_C.frg @@ -1,5 +1,6 @@ $PHE_C - 21 + 21 1 1 0 +PHE_C 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/PHE_N.frg b/src/data/charmm_s/PHE_N.frg index 24d1441a3b..f98010ad2f 100644 --- a/src/data/charmm_s/PHE_N.frg +++ b/src/data/charmm_s/PHE_N.frg @@ -1,5 +1,6 @@ $PHE_N - 22 + 22 1 1 0 +PHE_N 1 N NH3 0 0 1 1 -0.300000 0.000000 22H HC 0 0 1 1 0.330000 0.000000 33H HC 0 0 1 1 0.330000 0.000000 diff --git a/src/data/charmm_s/PRO.frg b/src/data/charmm_s/PRO.frg index c865a26637..b4f4fa833d 100644 --- a/src/data/charmm_s/PRO.frg +++ b/src/data/charmm_s/PRO.frg @@ -1,5 +1,6 @@ $PRO - 14 + 14 1 1 0 +PRO 1 N N 1 1 1 1 -0.290000 0.000000 2 CA CP1 0 0 1 1 0.020000 0.000000 3 HA HB 0 0 1 1 0.090000 0.000000 diff --git a/src/data/charmm_s/PRO_C.frg b/src/data/charmm_s/PRO_C.frg index 94eb7121f9..691bb31c90 100644 --- a/src/data/charmm_s/PRO_C.frg +++ b/src/data/charmm_s/PRO_C.frg @@ -1,5 +1,6 @@ $PRO_C - 15 + 15 1 1 0 +PRO_C 1 N N 1 1 1 1 -0.290000 0.000000 2 CA CP1 0 0 1 1 0.020000 0.000000 3 HA HB 0 0 1 1 0.090000 0.000000 diff --git a/src/data/charmm_s/PRO_N.frg b/src/data/charmm_s/PRO_N.frg index 1209210620..b615391f61 100644 --- a/src/data/charmm_s/PRO_N.frg +++ b/src/data/charmm_s/PRO_N.frg @@ -1,5 +1,6 @@ $PRO_N - 16 + 16 1 1 0 +PRO_N 1 N N 0 0 1 1 -0.070000 0.000000 22HN HC 0 0 1 1 0.240000 0.000000 33HN HC 0 0 1 1 0.240000 0.000000 diff --git a/src/data/charmm_s/SER.frg b/src/data/charmm_s/SER.frg index 64e57ee244..cdbc3a8038 100644 --- a/src/data/charmm_s/SER.frg +++ b/src/data/charmm_s/SER.frg @@ -1,5 +1,6 @@ $SER - 11 + 11 1 1 0 +SER 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/SER_C.frg b/src/data/charmm_s/SER_C.frg index e95d026605..e780026558 100644 --- a/src/data/charmm_s/SER_C.frg +++ b/src/data/charmm_s/SER_C.frg @@ -1,5 +1,6 @@ $SER_C - 12 + 12 1 1 0 +SER_C 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 @@ -22,4 +23,4 @@ $SER_C 5 8 8 9 10 11 - 10 12 \ No newline at end of file + 10 12 diff --git a/src/data/charmm_s/SER_N.frg b/src/data/charmm_s/SER_N.frg index 7a34c28c04..3b8f34f5e3 100644 --- a/src/data/charmm_s/SER_N.frg +++ b/src/data/charmm_s/SER_N.frg @@ -1,5 +1,6 @@ $SER_N - 13 + 13 1 1 0 +SER_N 1 N NH3 0 0 1 1 -0.300000 0.000000 22H HC 0 0 1 1 0.330000 0.000000 33H HC 0 0 1 1 0.330000 0.000000 diff --git a/src/data/charmm_s/THR.frg b/src/data/charmm_s/THR.frg index e4c6b9f191..94ebfa3d01 100644 --- a/src/data/charmm_s/THR.frg +++ b/src/data/charmm_s/THR.frg @@ -1,5 +1,6 @@ $THR - 14 + 14 1 1 0 +THR 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/THR_C.frg b/src/data/charmm_s/THR_C.frg index f3fbe63a9b..1150abeed6 100644 --- a/src/data/charmm_s/THR_C.frg +++ b/src/data/charmm_s/THR_C.frg @@ -1,5 +1,6 @@ $THR_C - 15 + 15 1 1 0 +THR_C 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/THR_N.frg b/src/data/charmm_s/THR_N.frg index 261c8c8f31..fb44a13732 100644 --- a/src/data/charmm_s/THR_N.frg +++ b/src/data/charmm_s/THR_N.frg @@ -1,5 +1,6 @@ $THR_N - 16 + 16 1 1 0 +THR_N 1 N NH3 0 0 1 1 -0.300000 0.000000 22H HC 0 0 1 1 0.330000 0.000000 33H HC 0 0 1 1 0.330000 0.000000 diff --git a/src/data/charmm_s/TIP3.frg b/src/data/charmm_s/TIP3.frg index 5a77c565db..033f88b76c 100644 --- a/src/data/charmm_s/TIP3.frg +++ b/src/data/charmm_s/TIP3.frg @@ -1,5 +1,6 @@ $TIP3 - 3 + 3 1 1 0 +TIP3 1 OH2 OT 0 0 1 1 -0.830000 0.000000 2 H1 HT 0 0 1 1 0.410000 0.000000 3 H2 HT 0 0 1 1 0.410000 0.000000 diff --git a/src/data/charmm_s/TP3M.frg b/src/data/charmm_s/TP3M.frg index c6c0a2001f..3a8be63d7f 100644 --- a/src/data/charmm_s/TP3M.frg +++ b/src/data/charmm_s/TP3M.frg @@ -1,5 +1,6 @@ $TP3M - 3 + 3 1 1 0 +TP3M 1 OH2 OT 0 0 1 1 -0.830000 0.000000 2 H1 HT 0 0 1 1 0.410000 0.000000 3 H2 HT 0 0 1 1 0.410000 0.000000 diff --git a/src/data/charmm_s/TRP.frg b/src/data/charmm_s/TRP.frg index c65cdf3897..60b24ee4c2 100644 --- a/src/data/charmm_s/TRP.frg +++ b/src/data/charmm_s/TRP.frg @@ -1,5 +1,6 @@ $TRP - 24 + 24 1 1 0 +TRP 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/TRP_C.frg b/src/data/charmm_s/TRP_C.frg index 5efa2d32ff..23b7eefd64 100644 --- a/src/data/charmm_s/TRP_C.frg +++ b/src/data/charmm_s/TRP_C.frg @@ -1,5 +1,6 @@ $TRP_C - 25 + 25 1 1 0 +TRP_C 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/TRP_N.frg b/src/data/charmm_s/TRP_N.frg index 51028f5627..17edb0391b 100644 --- a/src/data/charmm_s/TRP_N.frg +++ b/src/data/charmm_s/TRP_N.frg @@ -1,5 +1,6 @@ $TRP_N - 26 + 26 1 1 0 +TRP_N 1 N NH3 0 0 1 1 -0.300000 0.000000 22H HC 0 0 1 1 0.330000 0.000000 33H HC 0 0 1 1 0.330000 0.000000 diff --git a/src/data/charmm_s/TYR.frg b/src/data/charmm_s/TYR.frg index fd1d150127..12a4551d0e 100644 --- a/src/data/charmm_s/TYR.frg +++ b/src/data/charmm_s/TYR.frg @@ -1,5 +1,6 @@ $TYR - 21 + 21 1 1 0 +TYR 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/TYR_C.frg b/src/data/charmm_s/TYR_C.frg index 9964c38848..8cb6a6c80e 100644 --- a/src/data/charmm_s/TYR_C.frg +++ b/src/data/charmm_s/TYR_C.frg @@ -1,5 +1,6 @@ $TYR_C - 22 + 22 1 1 0 +TYR_C 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/TYR_N.frg b/src/data/charmm_s/TYR_N.frg index 61ccaa4e9b..aeb5927319 100644 --- a/src/data/charmm_s/TYR_N.frg +++ b/src/data/charmm_s/TYR_N.frg @@ -1,5 +1,6 @@ $TYR_N - 23 + 23 1 1 0 +TYR_N 1 N NH3 0 0 1 1 -0.300000 0.000000 22H HC 0 0 1 1 0.330000 0.000000 33H HC 0 0 1 1 0.330000 0.000000 diff --git a/src/data/charmm_s/VAL.frg b/src/data/charmm_s/VAL.frg index a8c915a380..c29bc103ff 100644 --- a/src/data/charmm_s/VAL.frg +++ b/src/data/charmm_s/VAL.frg @@ -1,5 +1,6 @@ $VAL - 16 + 16 1 1 0 +VAL 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/VAL_C.frg b/src/data/charmm_s/VAL_C.frg index 053970d6a0..d9dbe3690d 100644 --- a/src/data/charmm_s/VAL_C.frg +++ b/src/data/charmm_s/VAL_C.frg @@ -1,5 +1,6 @@ $VAL_C - 17 + 17 1 1 0 +VAL_C 1 N NH1 1 1 1 1 -0.470000 0.000000 2 H H 0 0 1 1 0.310000 0.000000 3 CA CT1 0 0 1 1 0.070000 0.000000 diff --git a/src/data/charmm_s/VAL_N.frg b/src/data/charmm_s/VAL_N.frg index 5bb97098b7..b618c4b3b7 100644 --- a/src/data/charmm_s/VAL_N.frg +++ b/src/data/charmm_s/VAL_N.frg @@ -1,5 +1,6 @@ -$VAL - 18 +$VAL_N + 18 1 1 0 +VAL_N 1 N NH3 0 0 1 1 -0.300000 0.000000 22H HC 0 0 1 1 0.330000 0.000000 33H HC 0 0 1 1 0.330000 0.000000 diff --git a/src/data/charmm_s/ZN2.frg b/src/data/charmm_s/ZN2.frg index 664ef394eb..8f556637fa 100644 --- a/src/data/charmm_s/ZN2.frg +++ b/src/data/charmm_s/ZN2.frg @@ -1,3 +1,4 @@ $ZN2 - 1 + 1 1 1 0 +ZN2 1 ZN ZN 0 0 1 1 2.000000 0.000000 diff --git a/src/data/charmm_x/GLU_C.frg b/src/data/charmm_x/GLU_C.frg index e269f280fd..f40dffddf4 100644 --- a/src/data/charmm_x/GLU_C.frg +++ b/src/data/charmm_x/GLU_C.frg @@ -3,7 +3,8 @@ # Atomic partial charges are crude guestimations # $GLU_C - 16 + 16 1 1 0 +GLU_C 1 N NH1 1 1 1 1 -0.179830 0.000000 2 H H 0 0 1 1 0.081563 0.000000 3 CA CT1 0 0 1 1 0.074962 0.000000 diff --git a/src/data/charmm_x/MET_N.frg b/src/data/charmm_x/MET_N.frg index 072300df3a..5d81bfa419 100644 --- a/src/data/charmm_x/MET_N.frg +++ b/src/data/charmm_x/MET_N.frg @@ -3,7 +3,8 @@ # Atomic partial charges are crude guestimations # $MET_N - 19 + 19 1 1 0 +MET_N 1 N NH3 0 0 1 1 0.114710 0.000000 22H HC 0 0 1 1 0.214756 0.000000 33H HC 0 0 1 1 0.199641 0.000000 diff --git a/src/data/charmm_x/Na.frg b/src/data/charmm_x/Na.frg index 04c476710d..9dd0ebfb19 100644 --- a/src/data/charmm_x/Na.frg +++ b/src/data/charmm_x/Na.frg @@ -2,6 +2,7 @@ # Atom types and connectivity were derived from coordinates # Atomic partial charges are crude guestimations # -$Na_M - 1 +$Na + 1 1 1 0 +Na 1Na Na 0 0 1 1 1.000000 0.000000 diff --git a/src/data/charmm_x/Na_M.frg b/src/data/charmm_x/Na_M.frg index 04c476710d..ed7e3ca4d5 100644 --- a/src/data/charmm_x/Na_M.frg +++ b/src/data/charmm_x/Na_M.frg @@ -3,5 +3,6 @@ # Atomic partial charges are crude guestimations # $Na_M - 1 + 1 1 1 0 +Na_M 1Na Na 0 0 1 1 1.000000 0.000000