From 94f7f7ccaa3bacd88288dae79d00baca7ed343d6 Mon Sep 17 00:00:00 2001 From: acmnpv Date: Thu, 13 Jul 2017 13:32:07 +0200 Subject: [PATCH] Fixes for OPLSAA2015 FF Changed to torsions in the parameter files for deprotonated arginine and lysine, with a bit better documentation how I got them. Also added capping residues used in ff validation calculations. --- ff/oplsaam2015/qoplsaa.lib | 2673 +++--------------------------------- ff/oplsaam2015/qoplsaa.prm | 99 +- 2 files changed, 226 insertions(+), 2546 deletions(-) diff --git a/ff/oplsaam2015/qoplsaa.lib b/ff/oplsaam2015/qoplsaa.lib index dff1837..60a1f14 100644 --- a/ff/oplsaam2015/qoplsaa.lib +++ b/ff/oplsaam2015/qoplsaa.lib @@ -45,6 +45,76 @@ CB HB1 HB2 HB3 C O *------------------------------------------------------------------ +{NAL} !charge: +1.00 || charged N terminal alanine -> for FF validation 10.1021/acs.jctc.5b00356 + [atoms] + 1 N N287 -0.300 + 2 HT1 H290 0.330 + 3 HT2 H290 0.330 + 4 HT3 H290 0.330 + 5 CA C293 0.250 + 6 HA H140 0.060 + 7 CB C135 -0.180 + 8 HB1 H140 0.060 + 9 HB2 H140 0.060 + 10 HB3 H140 0.060 + 11 C C235 0.500 + 12 O O236 -0.500 + [bonds] + CB CA + N HT1 + N HT2 + N HT3 + N CA + C CA + CA HA + CB HB1 + CB HB2 + CB HB3 + O C + [connections] + tail C + [impropers] + O C CA +N + [charge_groups] + N HT1 HT2 HT3 CA HA + CB HB1 HB2 HB3 + C O +*------------------------------------------------------------------ +{ALC} !charge: 0.00 || uncharged C-terminal alanine -> for FF validation 10.1021/acs.jctc.5b00356 + [atoms] + 1 N N238 -0.500 + 2 HN H241 0.300 + 3 CA C224 0.140 + 4 HA H140 0.060 + 5 CB C135 -0.180 + 6 HB1 H140 0.060 + 7 HB2 H140 0.060 + 8 HB3 H140 0.060 + 9 C C267 0.520 + 10 OT1 O269 -0.440 + 11 OT2 O268 -0.530 + 12 HT2 H270 0.450 + [bonds] + CB CA + N HN + N CA + C CA + CA HA + CB HB1 + CB HB2 + CB HB3 + OT1 C + OT2 C + OT2 HT2 + [connections] + head N + [impropers] + HN N -C CA + [charge_groups] + N HN CA HA + CB HB1 HB2 HB3 + C OT1 OT2 HT2 +*------------------------------------------------------------------ {ARG} !charge: 1.00 || [atoms] 1 N N238 -0.500 @@ -299,1250 +369,11 @@ N HN CA HA CB HB1 HB2 CG OD1 OD2 C O -!*------------------------------------------------------------------ -!{CALA} !charge: -1.1 || ALA C-terminal (standard) -! [atoms] -! 1 N N238 -0.500 -! 2 HN H241 0.300 -! 3 CA C285 -0.090 -! 4 HA H140 0.060 -! 5 CB C135 -0.180 -! 6 HB1 H140 0.060 -! 7 HB2 H140 0.060 -! 8 HB3 H140 0.060 -! 9 C C271 0.700 -! 10 OT1 O272 -0.800 -! 11 OT2 O272 -0.800 -! [bonds] -! CB CA -! N HN -! N CA -! C CA -! CA HA -! CB HB1 -! CB HB2 -! CB HB3 -! C OT2 -! C OT1 -! [connections] -! head N -! [impropers] -! HN N -C CA -! OT1 C CA OT2 -! [charge_groups] -! N HN CA HA -! CB HB1 HB2 HB3 -! C OT1 OT2 -!*------------------------------------------------------------------ -!{CARG} !charge: -0.1 || ARG C-terminal (standard) -! [atoms] -! 1 N N238 -0.500 -! 2 HN H241 0.300 -! 3 CA C285 -0.090 -! 4 HA H140 0.060 -! 5 CB C136 -0.120 -! 6 HB1 H140 0.060 -! 7 HB2 H140 0.060 -! 8 CG C308 -0.050 -! 9 HG1 H140 0.060 -! 10 HG2 H140 0.060 -! 11 CD C307 0.190 -! 12 HD1 H140 0.060 -! 13 HD2 H140 0.060 -! 14 NE N303 -0.700 -! 15 HE H304 0.440 -! 16 CZ C302 0.640 -! 17 NH1 N300 -0.800 -! 18 HH11 H301 0.460 -! 19 HH12 H301 0.460 -! 20 NH2 N300 -0.800 -! 21 HH21 H301 0.460 -! 22 HH22 H301 0.460 -! 23 C C271 0.700 -! 24 OT1 O272 -0.800 -! 25 OT2 O272 -0.800 -! [bonds] -! CB CA -! CG CB -! CD CG -! NE CD -! CZ NE -! NH2 CZ -! N HN -! N CA -! C CA -! CA HA -! CB HB1 -! CB HB2 -! CG HG1 -! CG HG2 -! CD HD1 -! CD HD2 -! NE HE -! NH1 HH11 -! NH1 HH12 -! NH2 HH21 -! NH2 HH22 -! CZ NH1 -! C OT2 -! C OT1 -! [connections] -! head N -! [impropers] -! HN N -C CA -! NH2 CZ NE NH1 -! HE NE CD CZ -! HH12 NH1 CZ HH11 -! HH22 NH2 CZ HH21 -! OT1 C CA OT2 -! [charge_groups] -! N HN CA HA -! CB HB1 HB2 -! CG HG1 HG2 CD HD1 HD2 NE HE CZ NH1 HH11 HH12 NH2 HH21 HH22 -! C OT1 OT2 -!*------------------------------------------------------------------ -!{CASH} !charge: -1.1 || ASH C-terminal (standard) -! [atoms] -! 1 N N238 -0.500 -! 2 HN H241 0.300 -! 3 CA C285 -0.090 -! 4 HA H140 0.060 -! 5 CB C136 -0.120 -! 6 HB1 H140 0.060 -! 7 HB2 H140 0.060 -! 8 CG C267 0.520 -! 9 OD1 O269 -0.440 -! 10 OD2 O268 -0.530 -! 11 C C271 0.700 -! 12 HD2 H270 0.450 -! 13 OT1 O272 -0.800 -! 14 OT2 O272 -0.800 -! [bonds] -! CB CA -! CG CB -! OD2 CG -! N HN -! N CA -! C CA -! C N -! CA HA -! CB HB1 -! CB HB2 -! CG OD1 -! OD2 HD2 -! C OT2 -! C OT1 -! [connections] -! head N -! [impropers] -! HN N -C CA -! OD2 CG CB OD1 -! OT1 C CA OT2 -! [charge_groups] -! N HN CA HA -! CB HB1 HB2 CG OD1 OD2 HD2 -! C OT1 OT2 -!*------------------------------------------------------------------ -!{CASN} !charge: -1.1 || ASN C-terminal (standard) -! [atoms] -! 1 N N238 -0.500 -! 2 HN H241 0.300 -! 3 CA C285 -0.090 -! 4 HA H140 0.060 -! 5 CB C136 -0.120 -! 6 HB1 H140 0.060 -! 7 HB2 H140 0.060 -! 8 CG C235 0.500 -! 9 OD1 O236 -0.500 -! 10 ND2 N237 -0.760 -! 11 HD21 H240 0.380 -! 12 HD22 H240 0.380 -! 13 C C271 0.700 -! 14 OT1 O272 -0.800 -! 15 OT2 O272 -0.800 -! [bonds] -! CB CA -! CG CB -! ND2 CG -! N HN -! N CA -! C CA -! CA HA -! CB HB1 -! CB HB2 -! ND2 HD21 -! ND2 HD22 -! CG OD1 -! C OT2 -! C OT1 -! [connections] -! head N -! [impropers] -! HN N -C CA -! OD1 CG CB ND2 -! HD22 ND2 CG HD21 -! OT1 C CA OT2 -! [charge_groups] -! N HN CA HA -! CB HB1 HB2 -! CG OD1 -! ND2 HD21 HD22 -! C OT1 OT2 -!*------------------------------------------------------------------ -!{CASP} !charge: -2.1 || ASP C-terminal (standard) -! [atoms] -! 1 N N238 -0.500 -! 2 HN H241 0.300 -! 3 CA C285 -0.090 -! 4 HA H140 0.060 -! 5 CB C274 -0.220 -! 6 HB1 H140 0.060 -! 7 HB2 H140 0.060 -! 8 CG C271 0.700 -! 9 OD1 O272 -0.800 -! 10 OD2 O272 -0.800 -! 11 C C271 0.700 -! 12 OT1 O272 -0.800 -! 13 OT2 O272 -0.800 -! [bonds] -! CB CA -! CG CB -! OD2 CG -! N HN -! N CA -! C CA -! CA HA -! CB HB1 -! CB HB2 -! CG OD1 -! C OT2 -! C OT1 -! [connections] -! head N -! [impropers] -! HN N -C CA -! OD2 CG CB OD1 -! OT1 C CA OT2 -! [charge_groups] -! N HN CA HA -! CB HB1 HB2 CG OD1 OD2 -! C OT1 OT2 -!*------------------------------------------------------------------ -!{CCYS} !charge: -1.1 || CYS C-terminal (standard) -! [atoms] -! 1 N N238 -0.500 -! 2 HN H241 0.300 -! 3 CA C285 -0.090 -! 4 HA H140 0.060 -! 5 CB C206 0.060 -! 6 HB1 H140 0.060 -! 7 HB2 H140 0.060 -! 8 SG S200 -0.335 -! 9 HG1 H204 0.155 -! 10 C C271 0.700 -! 11 OT1 O272 -0.800 -! 12 OT2 O272 -0.800 -! [bonds] -! CB CA -! SG CB -! N HN -! N CA -! C CA -! C N -! CA HA -! CB HB1 -! CB HB2 -! SG HG1 -! C OT2 -! C OT1 -! [connections] -! head N -! [impropers] -! HN N -C CA -! OT1 C CA OT2 -! [charge_groups] -! N HN CA HA -! CB HB1 HB2 SG HG1 -! C OT1 OT2 -!*------------------------------------------------------------------ -!{CCYX} !charge: -1.1 || CYX C-terminal (standard) -! [atoms] -! 1 N N238 -0.500 -! 2 HN H241 0.300 -! 3 CA C285 -0.090 -! 4 HA H140 0.060 -! 5 CB C214 0.0975 -! 6 HB1 H140 0.060 -! 7 HB2 H140 0.060 -! 8 SG S203 -0.2175 -! 9 C C271 0.700 -! 10 OT1 O272 -0.800 -! 11 OT2 O272 -0.800 -! [bonds] -! CB CA -! SG CB -! N HN -! N CA -! C CA -! CA HA -! CB HB1 -! CB HB2 -! C OT2 -! C OT1 -! [connections] -! head N -! [impropers] -! HN N -C CA -! OT1 C CA OT2 -! [charge_groups] -! N HN CA HA -! CB HB1 HB2 SG -! C OT1 OT2 -!*------------------------------------------------------------------ -!{CGLH} !charge: -1.1 || GLH C-terminal (standard) -! [atoms] -! 1 N N238 -0.500 -! 2 HN H241 0.300 -! 3 CA C285 -0.090 -! 4 HA H140 0.060 -! 5 CB C136 -0.120 -! 6 HB1 H140 0.060 -! 7 HB2 H140 0.060 -! 8 CG C136 -0.120 -! 9 HG1 H140 0.060 -! 10 HG2 H140 0.060 -! 11 CD C267 0.520 -! 12 OE1 O269 -0.440 -! 13 OE2 O268 -0.530 -! 14 C C271 0.700 -! 15 HE2 H270 0.450 -! 16 OT1 O272 -0.800 -! 17 OT2 O272 -0.800 -! [bonds] -! CB CA -! CG CB -! CD CG -! OE2 CD -! N HN -! N CA -! C CA -! CA HA -! CB HB1 -! CB HB2 -! CG HG1 -! CG HG2 -! CD OE1 -! OE2 HE2 -! C OT2 -! C OT1 -! [connections] -! head N -! [impropers] -! HN N -C CA -! OE2 CD CG OE1 -! OT1 C CA OT2 -! [charge_groups] -! N HN CA HA -! CB HB1 HB2 -! CG HG1 HG2 CD OE1 OE2 HE2 -! C OT1 OT2 -!*------------------------------------------------------------------ -!{CGLN} !charge: -1.1 || GLN C-terminal (standard) -! [atoms] -! 1 N N238 -0.500 -! 2 HN H241 0.300 -! 3 CA C285 -0.090 -! 4 HA H140 0.060 -! 5 CB C136 -0.120 -! 6 HB1 H140 0.060 -! 7 HB2 H140 0.060 -! 8 CG C136 -0.120 -! 9 HG1 H140 0.060 -! 10 HG2 H140 0.060 -! 11 CD C235 0.500 -! 12 OE1 O236 -0.500 -! 13 NE2 N237 -0.760 -! 14 HE21 H240 0.380 -! 15 HE22 H240 0.380 -! 16 C C271 0.700 -! 17 OT1 O272 -0.800 -! 18 OT2 O272 -0.800 -! [bonds] -! CB CA -! CG CB -! CD CG -! NE2 CD -! N HN -! N CA -! C CA -! CA HA -! CB HB1 -! CB HB2 -! CG HG1 -! CG HG2 -! NE2 HE21 -! NE2 HE22 -! CD OE1 -! C OT2 -! C OT1 -! [connections] -! head N -! [impropers] -! HN N -C CA -! OE1 CD CG NE2 -! HE22 NE2 CD HE21 -! OT1 C CA OT2 -! [charge_groups] -! N HN CA HA -! CB HB1 HB2 -! CG HG1 HG2 -! CD OE1 -! NE2 HE21 HE22 -! C OT1 OT2 -!*------------------------------------------------------------------ -!{CGLU} !charge: -2.1 || GLU C-terminal (standard) -! [atoms] -! 1 N N238 -0.500 -! 2 HN H241 0.300 -! 3 CA C285 -0.090 -! 4 HA H140 0.060 -! 5 CB C136 -0.120 -! 6 HB1 H140 0.060 -! 7 HB2 H140 0.060 -! 8 CG C274 -0.220 -! 9 HG1 H140 0.060 -! 10 HG2 H140 0.060 -! 11 CD C271 0.700 -! 12 OE1 O272 -0.800 -! 13 OE2 O272 -0.800 -! 14 C C271 0.700 -! 15 OT1 O272 -0.800 -! 16 OT2 O272 -0.800 -! [bonds] -! CB CA -! CG CB -! CD CG -! OE2 CD -! N HN -! N CA -! C CA -! CA HA -! CB HB1 -! CB HB2 -! CG HG1 -! CG HG2 -! CD OE1 -! C OT2 -! C OT1 -! [connections] -! head N -! [impropers] -! HN N -C CA -! OE2 CD CG OE1 -! OT1 C CA OT2 -! [charge_groups] -! N HN CA HA -! CB HB1 HB2 -! CG HG1 HG2 CD OE1 OE2 -! C OT1 OT2 -!*------------------------------------------------------------------ -!{CGLY} !charge: -1.1 || GLY C-terminal (standard) -! [atoms] -! 1 N N238 -0.500 -! 2 HN H241 0.300 -! 3 CA C285 -0.090 -! 4 HA1 H140 0.060 -! 5 HA2 H140 0.060 -! 6 C C271 0.700 -! 7 OT1 O272 -0.800 -! 8 OT2 O272 -0.800 -! [bonds] -! N HN -! N CA -! C CA -! C N -! CA HA1 -! CA HA2 -! C OT2 -! C OT1 -! [connections] -! head N -! [impropers] -! HN N -C CA -! OT1 C CA OT2 -! [charge_groups] -! N HN CA HA1 HA2 -! C OT1 OT2 -!*------------------------------------------------------------------ -!{CHID} !charge: -1.1 || HID C-terminal (standard) -! [atoms] -! 1 N N238 -0.500 -! 2 HN H241 0.300 -! 3 CA C285 -0.090 -! 4 HA H140 0.060 -! 5 CB C505 -0.005 -! 6 HB1 H140 0.060 -! 7 HB2 H140 0.060 -! 8 ND1 N503 -0.570 -! 9 HD1 H504 0.420 -! 10 CG C508 0.015 -! 11 CE1 C506 0.295 -! 12 HE1 H146 0.115 -! 13 NE2 N511 -0.490 -! 14 CD2 C507 -0.015 -! 15 HD2 H146 0.115 -! 16 C C271 0.700 -! 17 OT1 O272 -0.800 -! 18 OT2 O272 -0.800 -! [bonds] -! CB CA -! CG CB -! ND1 CG -! CE1 ND1 -! NE2 CD2 -! N HN -! N CA -! C CA -! CA HA -! CB HB1 -! CB HB2 -! ND1 HD1 -! CD2 HD2 -! CE1 HE1 -! CG CD2 -! CE1 NE2 -! C OT2 -! C OT1 -! [connections] -! head N -! [impropers] -! HD1 ND1 CG CE1 -! HD2 CD2 NE2 CG -! HE1 CE1 ND1 NE2 -! CB CG ND1 CD2 -! HN N -C CA -! OT1 C CA OT2 -! [charge_groups] -! N HN CA HA -! CB HB1 HB2 ND1 HD1 CG CE1 HE1 NE2 CD2 HD2 -! C OT1 OT2 -!*------------------------------------------------------------------ -!{CHIE} !charge: -1.1 || HIE C-terminal (standard) -! [atoms] -! 1 N N238 -0.500 -! 2 HN H241 0.300 -! 3 CA C285 -0.090 -! 4 HA H140 0.060 -! 5 CB C505 -0.005 -! 6 HB1 H140 0.060 -! 7 HB2 H140 0.060 -! 8 ND1 N511 -0.490 -! 9 CG C507 -0.015 -! 10 CE1 C506 0.295 -! 11 HE1 H146 0.115 -! 12 NE2 N503 -0.570 -! 13 HE2 H504 0.420 -! 14 CD2 C508 0.015 -! 15 HD2 H146 0.115 -! 16 C C271 0.700 -! 17 OT1 O272 -0.800 -! 18 OT2 O272 -0.800 -! [bonds] -! CB CA -! CG CB -! ND1 CG -! NE2 CD2 -! N HN -! N CA -! C CA -! NE2 CE1 -! CA HA -! CB HB1 -! CB HB2 -! NE2 HE2 -! CD2 HD2 -! CE1 HE1 -! CD2 CG -! CE1 ND1 -! C OT2 -! C OT1 -! [connections] -! head N -! [impropers] -! HE2 NE2 CE1 CD2 -! HD2 CD2 NE2 CG -! HE1 CE1 ND1 NE2 -! CB CG ND1 CD2 -! HN N -C CA -! OT1 C CA OT2 -! [charge_groups] -! N HN CA HA -! CB HB1 HB2 ND1 CG CE1 HE1 NE2 HE2 CD2 HD2 -! C OT1 OT2 -!*------------------------------------------------------------------ -!{CHIP} !charge: -0.1 || HIP C-terminal (standard) -! [atoms] -! 1 N N238 -0.500 -! 2 HN H241 0.300 -! 3 CA C285 -0.090 -! 4 HA H140 0.060 -! 5 CB C505 -0.005 -! 6 HB1 H140 0.060 -! 7 HB2 H140 0.060 -! 8 CD2 C510 0.215 -! 9 HD2 H146 0.115 -! 10 CG C510 0.215 -! 11 NE2 N512 -0.540 -! 12 HE2 H513 0.460 -! 13 ND1 N512 -0.540 -! 14 HD1 H513 0.460 -! 15 CE1 C509 0.385 -! 16 HE1 H146 0.115 -! 17 C C271 0.700 -! 18 OT1 O272 -0.800 -! 19 OT2 O272 -0.800 -! [bonds] -! CB CA -! CG CB -! ND1 CG -! CE1 ND1 -! NE2 CD2 -! N HN -! N CA -! C CA -! CA HA -! CB HB1 -! CB HB2 -! ND1 HD1 -! NE2 HE2 -! CD2 HD2 -! CE1 HE1 -! CD2 CG -! NE2 CE1 -! C OT2 -! C OT1 -! [connections] -! head N -! [impropers] -! HD1 ND1 CG CE1 -! HE1 CE1 ND1 NE2 -! HE2 NE2 CE1 CD2 -! HD2 CD2 NE2 CG -! CB CG ND1 CD2 -! HN N -C CA -! OT1 C CA OT2 -! [charge_groups] -! N HN CA HA -! CB HB1 HB2 CD2 HD2 CG NE2 HE2 ND1 HD1 CE1 HE1 -! C OT1 OT2 -!*------------------------------------------------------------------ -!{CILE} !charge: -1.1 || ILE C-terminal (standard) -! [atoms] -! 1 N N238 -0.500 -! 2 HN H241 0.300 -! 3 CA C285 -0.090 -! 4 HA H140 0.060 -! 5 CB C137 -0.060 -! 6 HB H140 0.060 -! 7 CG2 C135 -0.180 -! 8 HG21 H140 0.060 -! 9 HG22 H140 0.060 -! 10 HG23 H140 0.060 -! 11 CG1 C136 -0.120 -! 12 HG11 H140 0.060 -! 13 HG12 H140 0.060 -! 14 CD C135 -0.180 -! 15 HD1 H140 0.060 -! 16 HD2 H140 0.060 -! 17 HD3 H140 0.060 -! 18 C C271 0.700 -! 19 OT1 O272 -0.800 -! 20 OT2 O272 -0.800 -! [bonds] -! CB CA -! CG1 CB -! CG2 CB -! CD CG1 -! N HN -! N CA -! C CA -! CA HA -! CB HB -! CG1 HG11 -! CG1 HG12 -! CG2 HG21 -! CG2 HG22 -! CG2 HG23 -! CD HD1 -! CD HD2 -! CD HD3 -! C OT2 -! C OT1 -! [connections] -! head N -! [impropers] -! HN N -C CA -! OT1 C CA OT2 -! [charge_groups] -! N HN CA HA -! CB HB -! CG2 HG21 HG22 HG23 -! CG1 HG11 HG12 -! CD HD1 HD2 HD3 -! C OT1 OT2 *------------------------------------------------------------------ {CLA} !charge: -1.00 || Chloride Ion, adm jr. [atoms] 1 CLA CLA -1.00 *------------------------------------------------------------------ -!{CLEU} !charge: -1.1 || LEU C-terminal (standard) -! [atoms] -! 1 N N238 -0.500 -! 2 HN H241 0.300 -! 3 CA C285 -0.090 -! 4 HA H140 0.060 -! 5 CB C136 -0.120 -! 6 HB1 H140 0.060 -! 7 HB2 H140 0.060 -! 8 CG C137 -0.060 -! 9 HG H140 0.060 -! 10 CD1 C135 -0.180 -! 11 HD11 H140 0.060 -! 12 HD12 H140 0.060 -! 13 HD13 H140 0.060 -! 14 CD2 C135 -0.180 -! 15 HD21 H140 0.060 -! 16 HD22 H140 0.060 -! 17 HD23 H140 0.060 -! 18 C C271 0.700 -! 19 OT1 O272 -0.800 -! 20 OT2 O272 -0.800 -! [bonds] -! CB CA -! CG CB -! CD1 CG -! CD2 CG -! N HN -! N CA -! C CA -! CA HA -! CB HB1 -! CB HB2 -! CG HG -! CD1 HD11 -! CD1 HD12 -! CD1 HD13 -! CD2 HD21 -! CD2 HD22 -! CD2 HD23 -! C OT2 -! C OT1 -! [connections] -! head N -! [impropers] -! HN N -C CA -! OT1 C CA OT2 -! [charge_groups] -! N HN CA HA -! CB HB1 HB2 -! CG HG -! CD1 HD11 HD12 HD13 -! CD2 HD21 HD22 HD23 -! C OT1 OT2 -!*------------------------------------------------------------------ -!{CLYS} !charge: -0.1 || LYS C-terminal (standard) -! [atoms] -! 1 N N238 -0.500 -! 2 HN H241 0.300 -! 3 CA C285 -0.090 -! 4 HA H140 0.060 -! 5 CB C136 -0.120 -! 6 HB1 H140 0.060 -! 7 HB2 H140 0.060 -! 8 CG C136 -0.120 -! 9 HG1 H140 0.060 -! 10 HG2 H140 0.060 -! 11 CD C136 -0.120 -! 12 HD1 H140 0.060 -! 13 HD2 H140 0.060 -! 14 CE C292 0.190 -! 15 HE1 H140 0.060 -! 16 HE2 H140 0.060 -! 17 NZ N287 -0.300 -! 18 HZ1 H290 0.330 -! 19 HZ2 H290 0.330 -! 20 HZ3 H290 0.330 -! 21 C C271 0.700 -! 22 OT1 O272 -0.800 -! 23 OT2 O272 -0.800 -! [bonds] -! CB CA -! CG CB -! CD CG -! CE CD -! NZ CE -! N HN -! N CA -! C CA -! CA HA -! CB HB1 -! CB HB2 -! CG HG1 -! CG HG2 -! CD HD1 -! CD HD2 -! CE HE1 -! CE HE2 -! NZ HZ1 -! NZ HZ2 -! NZ HZ3 -! C OT2 -! C OT1 -! [connections] -! head N -! [impropers] -! HN N -C CA -! OT1 C CA OT2 -! [charge_groups] -! N HN CA HA -! CB HB1 HB2 -! CG HG1 HG2 -! CD HD1 HD2 -! CE HE1 HE2 NZ HZ1 HZ2 HZ3 -! C OT1 OT2 -!*------------------------------------------------------------------ -!{CMET} !charge: -1.1 || MET C-terminal (standard) -! [atoms] -! 1 N N238 -0.500 -! 2 HN H241 0.300 -! 3 CA C285 -0.090 -! 4 HA H140 0.060 -! 5 CB C136 -0.120 -! 6 HB1 H140 0.060 -! 7 HB2 H140 0.060 -! 8 CG C210 0.0475 -! 9 HG1 H140 0.060 -! 10 HG2 H140 0.060 -! 11 SD S202 -0.335 -! 12 CE C209 -0.0125 -! 13 HE1 H140 0.060 -! 14 HE2 H140 0.060 -! 15 HE3 H140 0.060 -! 16 C C271 0.700 -! 17 OT1 O272 -0.800 -! 18 OT2 O272 -0.800 -! [bonds] -! CB CA -! CG CB -! SD CG -! CE SD -! N HN -! N CA -! C CA -! CA HA -! CB HB1 -! CB HB2 -! CG HG1 -! CG HG2 -! CE HE1 -! CE HE2 -! CE HE3 -! C OT2 -! C OT1 -! [connections] -! head N -! [impropers] -! HN N -C CA -! OT1 C CA OT2 -! [charge_groups] -! N HN CA HA -! CB HB1 HB2 -! CG HG1 HG2 SD CE HE1 HE2 HE3 -! C OT1 OT2 -!*------------------------------------------------------------------ -!{CPHE} !charge: -1.1 || PHE C-terminal (standard) -! [atoms] -! 1 N N238 -0.500 -! 2 HN H241 0.300 -! 3 CA C285 -0.090 -! 4 HA H140 0.060 -! 5 CB C149 -0.005 -! 6 HB1 H140 0.060 -! 7 HB2 H140 0.060 -! 8 CG C145 -0.115 -! 9 CD1 C145 -0.115 -! 10 HD1 H146 0.115 -! 11 CE1 C145 -0.115 -! 12 HE1 H146 0.115 -! 13 CZ C145 -0.115 -! 14 HZ H146 0.115 -! 15 CD2 C145 -0.115 -! 16 HD2 H146 0.115 -! 17 CE2 C145 -0.115 -! 18 HE2 H146 0.115 -! 19 C C271 0.700 -! 20 OT1 O272 -0.800 -! 21 OT2 O272 -0.800 -! [bonds] -! CB CA -! CG CB -! CD2 CG -! CE1 CD1 -! CZ CE2 -! N HN -! N CA -! C CA -! CA HA -! CB HB1 -! CB HB2 -! CD1 HD1 -! CD2 HD2 -! CE1 HE1 -! CD1 CG -! CZ CE1 -! CE2 CD2 -! CE2 HE2 -! CZ HZ -! C OT2 -! C OT1 -! [connections] -! head N -! [impropers] -! HN N -C CA -! HD1 CD1 CG CE1 -! HE1 CE1 CD1 CZ -! HZ CZ CE1 CE2 -! CB CG CD1 CD2 -! HD2 CD2 CE2 CG -! HE2 CE2 CZ CD2 -! OT1 C CA OT2 -! [charge_groups] -! N HN CA HA -! CB HB1 HB2 CG -! CD1 HD1 -! CE1 HE1 -! CZ HZ -! CD2 HD2 -! CE2 HE2 -! C OT1 OT2 -!*------------------------------------------------------------------ -!{CPRO} !charge: -1.0 || PRO C-terminal (standard) -! [atoms] -! 1 N N239 -0.140 -! 2 CD C245 -0.050 -! 3 HD1 H140 0.060 -! 4 HD2 H140 0.060 -! 5 CA C285 -0.090 -! 6 HA H140 0.060 -! 7 CB C136 -0.120 -! 8 HB1 H140 0.060 -! 9 HB2 H140 0.060 -! 10 CG C136 -0.120 -! 11 HG1 H140 0.060 -! 12 HG2 H140 0.060 -! 13 C C271 0.700 -! 14 OT1 O272 -0.800 -! 15 OT2 O272 -0.800 -! [bonds] -! C CA -! N CA -! CA CB -! CB CG -! CG CD -! N CD -! HA CA -! HG1 CG -! HG2 CG -! HD1 CD -! HD2 CD -! HB1 CB -! HB2 CB -! C OT2 -! C OT1 -! [connections] -! head N -! [impropers] -! CD N -C CA -! OT1 C CA OT2 -! [charge_groups] -! N CD HD1 HD2 CA HA -! CB HB1 HB2 -! CG HG1 HG2 -! C OT1 OT2 -!*------------------------------------------------------------------ -!{CSER} !charge: -1.1 || SER C-terminal (standard) -! [atoms] -! 1 N N238 -0.500 -! 2 HN H241 0.300 -! 3 CA C285 -0.090 -! 4 HA H140 0.060 -! 5 CB C157 0.145 -! 6 HB1 H140 0.060 -! 7 HB2 H140 0.060 -! 8 OG O154 -0.683 -! 9 HG1 H155 0.418 -! 10 C C271 0.700 -! 11 OT1 O272 -0.800 -! 12 OT2 O272 -0.800 -! [bonds] -! CB CA -! OG CB -! N HN -! N CA -! C CA -! CA HA -! CB HB1 -! CB HB2 -! OG HG1 -! C OT2 -! C OT1 -! [connections] -! head N -! [impropers] -! HN N -C CA -! OT1 C CA OT2 -! [charge_groups] -! N HN CA HA -! CB HB1 HB2 OG HG1 -! C OT1 OT2 -!*------------------------------------------------------------------ -!{CTHR} !charge: -1.1 || THR C-terminal (standard) -! [atoms] -! 1 N N238 -0.500 -! 2 HN H241 0.300 -! 3 CA C285 -0.090 -! 4 HA H140 0.060 -! 5 CB C158 0.205 -! 6 HB H140 0.060 -! 7 OG1 O154 -0.683 -! 8 HG1 H155 0.418 -! 9 CG2 C135 -0.180 -! 10 HG21 H140 0.060 -! 11 HG22 H140 0.060 -! 12 HG23 H140 0.060 -! 13 C C271 0.700 -! 14 OT1 O272 -0.800 -! 15 OT2 O272 -0.800 -! [bonds] -! CB CA -! OG1 CB -! CG2 CB -! N HN -! N CA -! C CA -! CA HA -! CB HB -! OG1 HG1 -! CG2 HG21 -! CG2 HG22 -! CG2 HG23 -! C OT2 -! C OT1 -! [connections] -! head N -! [impropers] -! HN N -C CA -! OT1 C CA OT2 -! [charge_groups] -! N HN CA HA -! CB HB OG1 HG1 -! CG2 HG21 HG22 HG23 -! C OT1 OT2 -!*------------------------------------------------------------------ -!{CTRP} !charge: -1.1 || TRP C-terminal (standard) -! [atoms] -! 1 N N238 -0.500 -! 2 HN H241 0.300 -! 3 CA C285 -0.090 -! 4 HA H140 0.060 -! 5 CB C136 -0.120 -! 6 HB1 H140 0.060 -! 7 HB2 H140 0.060 -! 8 CG C500 0.075 -! 9 CD1 C514 -0.115 -! 10 HD1 H146 0.115 -! 11 NE1 N503 -0.570 -! 12 HE1 H504 0.420 -! 13 CE2 C502 0.130 -! 14 CD2 C501 -0.055 -! 15 CE3 C145 -0.115 -! 16 HE3 H146 0.115 -! 17 CZ3 C145 -0.115 -! 18 HZ3 H146 0.115 -! 19 CZ2 C145 -0.115 -! 20 HZ2 H146 0.115 -! 21 CH2 C145 -0.115 -! 22 HH2 H146 0.115 -! 23 C C271 0.700 -! 24 OT1 O272 -0.800 -! 25 OT2 O272 -0.800 -! [bonds] -! CB CA -! CG CB -! CD2 CG -! NE1 CD1 -! CZ2 CE2 -! N HN -! N CA -! C CA -! CZ3 CH2 -! CD2 CE3 -! NE1 CE2 -! CA HA -! CB HB1 -! CB HB2 -! CD1 HD1 -! NE1 HE1 -! CE3 HE3 -! CZ2 HZ2 -! CZ3 HZ3 -! CH2 HH2 -! CD1 CG -! CE2 CD2 -! CZ3 CE3 -! CH2 CZ2 -! C OT2 -! C OT1 -! [connections] -! head N -! [impropers] -! HN N -C CA -! CB CG CD1 CD2 -! HD1 CD1 CG NE1 -! HE1 NE1 CD1 CE2 -! HZ2 CZ2 CE2 CH2 -! HH2 CH2 CZ2 CZ3 -! HZ3 CZ3 CH2 CE3 -! HE3 CE3 CZ3 CD2 -! CE2 CD2 CE3 CG -! CZ2 CE2 CD2 NE1 -! OT1 C CA OT2 -! [charge_groups] -! N HN CA HA -! CB HB1 HB2 -! CG CD1 HD1 NE1 HE1 CE2 CD2 -! CE3 HE3 -! CZ3 HZ3 -! CZ2 HZ2 -! CH2 HH2 -! C OT1 OT2 -!*------------------------------------------------------------------ -!{CTYR} !charge: -1.1 || TYR C-terminal (standard) -! [atoms] -! 1 N N238 -0.500 -! 2 HN H241 0.300 -! 3 CA C285 -0.090 -! 4 HA H140 0.060 -! 5 CB C149 -0.005 -! 6 HB1 H140 0.060 -! 7 HB2 H140 0.060 -! 8 CG C145 -0.115 -! 9 CD1 C145 -0.115 -! 10 HD1 H146 0.115 -! 11 CE1 C145 -0.115 -! 12 HE1 H146 0.115 -! 13 CZ C166 0.150 -! 14 OH O167 -0.585 -! 15 HH H168 0.435 -! 16 CD2 C145 -0.115 -! 17 HD2 H146 0.115 -! 18 CE2 C145 -0.115 -! 19 HE2 H146 0.115 -! 20 C C271 0.700 -! 21 OT1 O272 -0.800 -! 22 OT2 O272 -0.800 -! [bonds] -! CB CA -! CG CB -! CD2 CG -! CE1 CD1 -! CZ CE2 -! OH CZ -! N HN -! N CA -! C CA -! CA HA -! CB HB1 -! CB HB2 -! CD1 HD1 -! CD2 HD2 -! CE1 HE1 -! CE2 HE2 -! OH HH -! CD1 CG -! CE1 CZ -! CE2 CD2 -! C OT2 -! C OT1 -! [connections] -! head N -! [impropers] -! HN N -C CA -! HD1 CD1 CG CE1 -! HE1 CE1 CD1 CZ -! OH CZ CE1 CE2 -! CB CG CD1 CD2 -! HD2 CD2 CE2 CG -! HE2 CE2 CZ CD2 -! OT1 C CA OT2 -! [charge_groups] -! N HN CA HA -! CB HB1 HB2 CG -! CD1 HD1 -! CE1 HE1 -! CZ OH HH -! CD2 HD2 -! CE2 HE2 -! C OT1 OT2 -!*------------------------------------------------------------------ -!{CVAL} !charge: -1.1 || VAL C-terminal (standard) -! [atoms] -! 1 N N238 -0.500 -! 2 HN H241 0.300 -! 3 CA C285 -0.090 -! 4 HA H140 0.060 -! 5 CB C137 -0.060 -! 6 HB H140 0.060 -! 7 CG1 C135 -0.180 -! 8 HG11 H140 0.060 -! 9 HG12 H140 0.060 -! 10 HG13 H140 0.060 -! 11 CG2 C135 -0.180 -! 12 HG21 H140 0.060 -! 13 HG22 H140 0.060 -! 14 HG23 H140 0.060 -! 15 C C271 0.700 -! 16 OT1 O272 -0.800 -! 17 OT2 O272 -0.800 -! [bonds] -! CB CA -! CG1 CB -! CG2 CB -! N HN -! N CA -! C CA -! CA HA -! CB HB -! CG1 HG11 -! CG1 HG12 -! CG1 HG13 -! CG2 HG21 -! CG2 HG22 -! CG2 HG23 -! C OT2 -! C OT1 -! [connections] -! head N -! [impropers] -! HN N -C CA -! OT1 C CA OT2 -! [charge_groups] -! N HN CA HA -! CB HB -! CG1 HG11 HG12 HG13 -! CG2 HG21 HG22 HG23 -! C OT1 OT2 -*------------------------------------------------------------------ {CYS} !charge: 0.00 || [atoms] 1 N N238 -0.500 @@ -1781,6 +612,62 @@ N HN CA HA1 HA2 C O *------------------------------------------------------------------ +{NGL} !charge: +1.00 || N-terminal Glycine -> for FF validation 10.1021/acs.jctc.5b00356 + [atoms] + 1 N N287 -0.300 + 2 HT1 H290 0.330 + 3 HT2 H290 0.330 + 4 HT3 H290 0.330 + 5 CA C292 0.190 + 6 HA1 H140 0.060 + 7 HA2 H140 0.060 + 8 C C235 0.500 + 9 O O236 -0.500 + [bonds] + N HT1 + N HT2 + N HT3 + N CA + C CA + CA HA1 + CA HA2 + O C + [connections] + tail C + [impropers] + O C CA +N + [charge_groups] + N HT1 HT2 HT3 CA HA1 HA2 + C O +*------------------------------------------------------------------ +{GLC} !charge: 0.00 || uncharged C-terminal GLycine -> for FF validation 10.1021/acs.jctc.5b00356 + [atoms] + 1 N N238 -0.500 + 2 HN H241 0.300 + 3 CA C223 0.080 + 4 HA1 H140 0.060 + 5 HA2 H140 0.060 + 6 C C267 0.520 + 7 OT1 O269 -0.440 + 8 OT2 O268 -0.530 + 9 HT2 H270 0.450 + [bonds] + N HN + N CA + C CA + CA HA1 + CA HA2 + OT1 C + OT2 C + OT2 HT2 + [connections] + head N + [impropers] + HN N -C CA + [charge_groups] + N HN CA HA1 HA2 + C OT1 OT2 HT2 +*------------------------------------------------------------------ {HID} !charge: 0.00 || neutral HIS, proton on ND1 [atoms] 1 N N238 -0.500 @@ -2217,1267 +1104,6 @@ CG HG1 HG2 SD CE HE1 HE2 HE3 C O *------------------------------------------------------------------ -!{NALA} !charge: 1.0 || ALA N-terminal (standard) -! [atoms] -! 1 N N287 -0.300 -! 2 CA C293 0.250 -! 3 HA H140 0.060 -! 4 CB C135 -0.180 -! 5 HB1 H140 0.060 -! 6 HB2 H140 0.060 -! 7 HB3 H140 0.060 -! 8 C C235 0.500 -! 9 O O236 -0.500 -! 10 HT1 H290 0.330 -! 11 HT2 H290 0.330 -! 12 HT3 H290 0.330 -! [bonds] -! CB CA -! N CA -! C CA -! CA HA -! CB HB1 -! CB HB2 -! CB HB3 -! O C -! HT1 N -! HT2 N -! HT3 N -! [connections] -! tail C -! [impropers] -! O C CA +N -! [charge_groups] -! N HT1 HT2 HT3 CA HA -! CB HB1 HB2 HB3 -! C O -!*------------------------------------------------------------------ -!{NARG} !charge: 2.0 || ARG N-terminal (standard) -! [atoms] -! 1 N N287 -0.300 -! 2 CA C293 0.250 -! 3 HA H140 0.060 -! 4 CB C136 -0.120 -! 5 HB1 H140 0.060 -! 6 HB2 H140 0.060 -! 7 CG C308 -0.050 -! 8 HG1 H140 0.060 -! 9 HG2 H140 0.060 -! 10 CD C307 0.190 -! 11 HD1 H140 0.060 -! 12 HD2 H140 0.060 -! 13 NE N303 -0.700 -! 14 HE H304 0.440 -! 15 CZ C302 0.640 -! 16 NH1 N300 -0.800 -! 17 HH11 H301 0.460 -! 18 HH12 H301 0.460 -! 19 NH2 N300 -0.800 -! 20 HH21 H301 0.460 -! 21 HH22 H301 0.460 -! 22 C C235 0.500 -! 23 O O236 -0.500 -! 24 HT1 H290 0.330 -! 25 HT2 H290 0.330 -! 26 HT3 H290 0.330 -! [bonds] -! CB CA -! CG CB -! CD CG -! NE CD -! CZ NE -! NH2 CZ -! N CA -! C CA -! CA HA -! CB HB1 -! CB HB2 -! CG HG1 -! CG HG2 -! CD HD1 -! CD HD2 -! NE HE -! NH1 HH11 -! NH1 HH12 -! NH2 HH21 -! NH2 HH22 -! O C -! CZ NH1 -! HT1 N -! HT2 N -! HT3 N -! [connections] -! tail C -! [impropers] -! O C CA +N -! NH2 CZ NE NH1 -! HE NE CD CZ -! HH12 NH1 CZ HH11 -! HH22 NH2 CZ HH21 -! [charge_groups] -! N HT1 HT2 HT3 CA HA -! CB HB1 HB2 -! CG HG1 HG2 CD HD1 HD2 NE HE CZ NH1 HH11 HH12 NH2 HH21 HH22 -! C O -!*------------------------------------------------------------------ -!{NASH} !charge: 1.0 || ASH N-terminal (standard) -! [atoms] -! 1 N N287 -0.300 -! 2 CA C293 0.250 -! 3 HA H140 0.060 -! 4 CB C136 -0.120 -! 5 HB1 H140 0.060 -! 6 HB2 H140 0.060 -! 7 CG C267 0.520 -! 8 OD1 O269 -0.440 -! 9 OD2 O268 -0.530 -! 10 C C235 0.500 -! 11 O O236 -0.500 -! 12 HD2 H270 0.450 -! 13 HT1 H290 0.330 -! 14 HT2 H290 0.330 -! 15 HT3 H290 0.330 -! [bonds] -! CB CA -! CG CB -! OD2 CG -! N CA -! C CA -! CA HA -! CB HB1 -! CB HB2 -! O C -! CG OD1 -! OD2 HD2 -! HT1 N -! HT2 N -! HT3 N -! [connections] -! tail C -! [impropers] -! O C CA +N -! OD2 CG CB OD1 -! [charge_groups] -! N HT1 HT2 HT3 CA HA -! CB HB1 HB2 CG OD1 OD2 HD2 -! C O -!*------------------------------------------------------------------ -!{NASN} !charge: 1.0 || ASN N-terminal (standard) -! [atoms] -! 1 N N287 -0.300 -! 2 CA C293 0.250 -! 3 HA H140 0.060 -! 4 CB C136 -0.120 -! 5 HB1 H140 0.060 -! 6 HB2 H140 0.060 -! 7 CG C235 0.500 -! 8 OD1 O236 -0.500 -! 9 ND2 N237 -0.760 -! 10 HD21 H240 0.380 -! 11 HD22 H240 0.380 -! 12 C C235 0.500 -! 13 O O236 -0.500 -! 14 HT1 H290 0.330 -! 15 HT2 H290 0.330 -! 16 HT3 H290 0.330 -! [bonds] -! CB CA -! CG CB -! ND2 CG -! N CA -! C CA -! CA HA -! CB HB1 -! CB HB2 -! ND2 HD21 -! ND2 HD22 -! C O -! CG OD1 -! HT1 N -! HT2 N -! HT3 N -! [connections] -! tail C -! [impropers] -! O C CA +N -! OD1 CG CB ND2 -! HD22 ND2 CG HD21 -! [charge_groups] -! N HT1 HT2 HT3 CA HA -! CB HB1 HB2 -! CG OD1 -! ND2 HD21 HD22 -! C O -!*------------------------------------------------------------------ -!{NASP} !charge: -0.0 || ASP N-terminal (standard) -! [atoms] -! 1 N N287 -0.300 -! 2 CA C293 0.250 -! 3 HA H140 0.060 -! 4 CB C274 -0.220 -! 5 HB1 H140 0.060 -! 6 HB2 H140 0.060 -! 7 CG C271 0.700 -! 8 OD1 O272 -0.800 -! 9 OD2 O272 -0.800 -! 10 C C235 0.500 -! 11 O O236 -0.500 -! 12 HT1 H290 0.330 -! 13 HT2 H290 0.330 -! 14 HT3 H290 0.330 -! [bonds] -! CB CA -! CG CB -! OD2 CG -! N CA -! C CA -! CA HA -! CB HB1 -! CB HB2 -! O C -! CG OD1 -! HT1 N -! HT2 N -! HT3 N -! [connections] -! tail C -! [impropers] -! O C CA +N -! OD2 CG CB OD1 -! [charge_groups] -! N HT1 HT2 HT3 CA HA -! CB HB1 HB2 CG OD1 OD2 -! C O -!*------------------------------------------------------------------ -!{NCYS} !charge: 1.0 || CYS N-terminal (standard) -! [atoms] -! 1 N N287 -0.300 -! 2 CA C293 0.250 -! 3 HA H140 0.060 -! 4 CB C206 0.060 -! 5 HB1 H140 0.060 -! 6 HB2 H140 0.060 -! 7 SG S200 -0.335 -! 8 HG1 H204 0.155 -! 9 C C235 0.500 -! 10 O O236 -0.500 -! 11 HT1 H290 0.330 -! 12 HT2 H290 0.330 -! 13 HT3 H290 0.330 -! [bonds] -! CB CA -! SG CB -! N CA -! C CA -! CA HA -! CB HB1 -! CB HB2 -! SG HG1 -! O C -! HT1 N -! HT2 N -! HT3 N -! [connections] -! tail C -! [impropers] -! O C CA +N -! [charge_groups] -! N HT1 HT2 HT3 CA HA -! CB HB1 HB2 SG HG1 -! C O -!*------------------------------------------------------------------ -!{NCYX} !charge: 1.0 || CYX N-terminal (standard) -! [atoms] -! 1 N N287 -0.300 -! 2 CA C293 0.250 -! 3 HA H140 0.060 -! 4 CB C214 0.0975 -! 5 HB1 H140 0.060 -! 6 HB2 H140 0.060 -! 7 SG S203 -0.2175 -! 8 C C235 0.500 -! 9 O O236 -0.500 -! 10 HT1 H290 0.330 -! 11 HT2 H290 0.330 -! 12 HT3 H290 0.330 -! [bonds] -! CB CA -! SG CB -! N CA -! C CA -! CA HA -! CB HB1 -! CB HB2 -! O C -! HT1 N -! HT2 N -! HT3 N -! [connections] -! tail C -! [impropers] -! O C CA +N -! [charge_groups] -! N HT1 HT2 HT3 CA HA -! CB HB1 HB2 SG -! C O -!*------------------------------------------------------------------ -!{NGLH} !charge: 1.0 || GLH N-terminal (standard) -! [atoms] -! 1 N N287 -0.300 -! 2 CA C293 0.250 -! 3 HA H140 0.060 -! 4 CB C136 -0.120 -! 5 HB1 H140 0.060 -! 6 HB2 H140 0.060 -! 7 CG C136 -0.120 -! 8 HG1 H140 0.060 -! 9 HG2 H140 0.060 -! 10 CD C267 0.520 -! 11 OE1 O269 -0.440 -! 12 OE2 O268 -0.530 -! 13 C C235 0.500 -! 14 O O236 -0.500 -! 15 HE2 H270 0.450 -! 16 HT1 H290 0.330 -! 17 HT2 H290 0.330 -! 18 HT3 H290 0.330 -! [bonds] -! CB CA -! CG CB -! CD CG -! OE2 CD -! N CA -! C CA -! CA HA -! CB HB1 -! CB HB2 -! CG HG1 -! CG HG2 -! O C -! CD OE1 -! OE2 HE2 -! HT1 N -! HT2 N -! HT3 N -! [connections] -! tail C -! [impropers] -! O C CA +N -! OE2 CD CG OE1 -! [charge_groups] -! N HT1 HT2 HT3 CA HA -! CB HB1 HB2 -! CG HG1 HG2 CD OE1 OE2 HE2 -! C O -!*------------------------------------------------------------------ -!{NGLN} !charge: 1.0 || GLN N-terminal (standard) -! [atoms] -! 1 N N287 -0.300 -! 2 CA C293 0.250 -! 3 HA H140 0.060 -! 4 CB C136 -0.120 -! 5 HB1 H140 0.060 -! 6 HB2 H140 0.060 -! 7 CG C136 -0.120 -! 8 HG1 H140 0.060 -! 9 HG2 H140 0.060 -! 10 CD C235 0.500 -! 11 OE1 O236 -0.500 -! 12 NE2 N237 -0.760 -! 13 HE21 H240 0.380 -! 14 HE22 H240 0.380 -! 15 C C235 0.500 -! 16 O O236 -0.500 -! 17 HT1 H290 0.330 -! 18 HT2 H290 0.330 -! 19 HT3 H290 0.330 -! [bonds] -! CB CA -! CG CB -! CD CG -! NE2 CD -! N CA -! C CA -! CA HA -! CB HB1 -! CB HB2 -! CG HG1 -! CG HG2 -! NE2 HE21 -! NE2 HE22 -! O C -! CD OE1 -! HT1 N -! HT2 N -! HT3 N -! [connections] -! tail C -! [impropers] -! O C CA +N -! OE1 CD CG NE2 -! HE22 NE2 CD HE21 -! [charge_groups] -! N HT1 HT2 HT3 CA HA -! CB HB1 HB2 -! CG HG1 HG2 -! CD OE1 -! NE2 HE21 HE22 -! C O -!*------------------------------------------------------------------ -!{NGLU} !charge: -0.0 || GLU N-terminal (standard) -! [atoms] -! 1 N N287 -0.300 -! 2 CA C293 0.250 -! 3 HA H140 0.060 -! 4 CB C136 -0.120 -! 5 HB1 H140 0.060 -! 6 HB2 H140 0.060 -! 7 CG C274 -0.220 -! 8 HG1 H140 0.060 -! 9 HG2 H140 0.060 -! 10 CD C271 0.700 -! 11 OE1 O272 -0.800 -! 12 OE2 O272 -0.800 -! 13 C C235 0.500 -! 14 O O236 -0.500 -! 15 HT1 H290 0.330 -! 16 HT2 H290 0.330 -! 17 HT3 H290 0.330 -! [bonds] -! CB CA -! CG CB -! CD CG -! OE2 CD -! N CA -! C CA -! CA HA -! CB HB1 -! CB HB2 -! CG HG1 -! CG HG2 -! O C -! CD OE1 -! HT1 N -! HT2 N -! HT3 N -! [connections] -! tail C -! [impropers] -! O C CA +N -! OE2 CD CG OE1 -! [charge_groups] -! N HT1 HT2 HT3 CA HA -! CB HB1 HB2 -! CG HG1 HG2 CD OE1 OE2 -! C O -!*------------------------------------------------------------------ -!{NGLY} !charge: 1.1 || GLY N-terminal (standard) -! [atoms] -! 1 N N287 -0.300 -! 2 CA C293 0.250 -! 3 HA1 H140 0.060 -! 4 HA2 H140 0.060 -! 5 C C235 0.500 -! 6 O O236 -0.500 -! 7 HT1 H290 0.330 -! 8 HT2 H290 0.330 -! 9 HT3 H290 0.330 -! [bonds] -! N CA -! C CA -! CA HA1 -! CA HA2 -! O C -! HT1 N -! HT2 N -! HT3 N -! [connections] -! tail C -! [impropers] -! O C CA +N -! [charge_groups] -! N HT1 HT2 HT3 CA HA1 HA2 -! C O -!*------------------------------------------------------------------ -!{NHID} !charge: 1.0 || HID N-terminal (standard) -! [atoms] -! 1 N N287 -0.300 -! 2 CA C293 0.250 -! 3 HA H140 0.060 -! 4 CB C505 -0.005 -! 5 HB1 H140 0.060 -! 6 HB2 H140 0.060 -! 7 ND1 N503 -0.570 -! 8 HD1 H504 0.420 -! 9 CG C508 0.015 -! 10 CE1 C506 0.295 -! 11 HE1 H146 0.115 -! 12 NE2 N511 -0.490 -! 13 CD2 C507 -0.015 -! 14 HD2 H146 0.115 -! 15 C C235 0.500 -! 16 O O236 -0.500 -! 17 HT1 H290 0.330 -! 18 HT2 H290 0.330 -! 19 HT3 H290 0.330 -! [bonds] -! CB CA -! CG CB -! ND1 CG -! CE1 ND1 -! NE2 CD2 -! N CA -! C CA -! CA HA -! CB HB1 -! CB HB2 -! ND1 HD1 -! CD2 HD2 -! CE1 HE1 -! O C -! CG CD2 -! CE1 NE2 -! HT1 N -! HT2 N -! HT3 N -! [connections] -! tail C -! [impropers] -! HD1 ND1 CG CE1 -! HD2 CD2 NE2 CG -! HE1 CE1 ND1 NE2 -! CB CG ND1 CD2 -! O C CA +N -! [charge_groups] -! N HT1 HT2 HT3 CA HA -! CB HB1 HB2 ND1 HD1 CG CE1 HE1 NE2 CD2 HD2 -! C O -!*------------------------------------------------------------------ -!{NHIE} !charge: 1.0 || HIE N-terminal (standard) -! [atoms] -! 1 N N287 -0.300 -! 2 CA C293 0.250 -! 3 HA H140 0.060 -! 4 CB C505 -0.005 -! 5 HB1 H140 0.060 -! 6 HB2 H140 0.060 -! 7 ND1 N511 -0.490 -! 8 CG C507 -0.015 -! 9 CE1 C506 0.295 -! 10 HE1 H146 0.115 -! 11 NE2 N503 -0.570 -! 12 HE2 H504 0.420 -! 13 CD2 C508 0.015 -! 14 HD2 H146 0.115 -! 15 C C235 0.500 -! 16 O O236 -0.500 -! 17 HT1 H290 0.330 -! 18 HT2 H290 0.330 -! 19 HT3 H290 0.330 -! [bonds] -! CB CA -! CG CB -! ND1 CG -! NE2 CD2 -! N CA -! C CA -! NE2 CE1 -! CA HA -! CB HB1 -! CB HB2 -! NE2 HE2 -! CD2 HD2 -! CE1 HE1 -! O C -! CD2 CG -! CE1 ND1 -! HT1 N -! HT2 N -! HT3 N -! [connections] -! tail C -! [impropers] -! HE2 NE2 CE1 CD2 -! HD2 CD2 NE2 CG -! HE1 CE1 ND1 NE2 -! CB CG ND1 CD2 -! O C CA +N -! [charge_groups] -! N HT1 HT2 HT3 CA HA -! CB HB1 HB2 ND1 CG CE1 HE1 NE2 HE2 CD2 HD2 -! C O -!*------------------------------------------------------------------ -!{NHIP} !charge: 2.0 || HIP N-terminal (standard) -! [atoms] -! 1 N N287 -0.300 -! 2 CA C293 0.250 -! 3 HA H140 0.060 -! 4 CB C505 -0.005 -! 5 HB1 H140 0.060 -! 6 HB2 H140 0.060 -! 7 CD2 C510 0.215 -! 8 HD2 H146 0.115 -! 9 CG C510 0.215 -! 10 NE2 N512 -0.540 -! 11 HE2 H513 0.460 -! 12 ND1 N512 -0.540 -! 13 HD1 H513 0.460 -! 14 CE1 C509 0.385 -! 15 HE1 H146 0.115 -! 16 C C235 0.500 -! 17 O O236 -0.500 -! 18 HT1 H290 0.330 -! 19 HT2 H290 0.330 -! 20 HT3 H290 0.330 -! [bonds] -! CB CA -! CG CB -! ND1 CG -! CE1 ND1 -! NE2 CD2 -! N CA -! C CA -! CA HA -! CB HB1 -! CB HB2 -! ND1 HD1 -! NE2 HE2 -! CD2 HD2 -! CE1 HE1 -! O C -! CD2 CG -! NE2 CE1 -! HT1 N -! HT2 N -! HT3 N -! [connections] -! tail C -! [impropers] -! HD1 ND1 CG CE1 -! HE1 CE1 ND1 NE2 -! HE2 NE2 CE1 CD2 -! HD2 CD2 NE2 CG -! CB CG ND1 CD2 -! O C CA +N -! [charge_groups] -! N HT1 HT2 HT3 CA HA -! CB HB1 HB2 CD2 HD2 CG NE2 HE2 ND1 HD1 CE1 HE1 -! C O -!*------------------------------------------------------------------ -!{NILE} !charge: 1.0 || ILE N-terminal (standard) -! [atoms] -! 1 N N287 -0.300 -! 2 CA C293 0.250 -! 3 HA H140 0.060 -! 4 CB C137 -0.060 -! 5 HB H140 0.060 -! 6 CG2 C135 -0.180 -! 7 HG21 H140 0.060 -! 8 HG22 H140 0.060 -! 9 HG23 H140 0.060 -! 10 CG1 C136 -0.120 -! 11 HG11 H140 0.060 -! 12 HG12 H140 0.060 -! 13 CD C135 -0.180 -! 14 HD1 H140 0.060 -! 15 HD2 H140 0.060 -! 16 HD3 H140 0.060 -! 17 C C235 0.500 -! 18 O O236 -0.500 -! 19 HT1 H290 0.330 -! 20 HT2 H290 0.330 -! 21 HT3 H290 0.330 -! [bonds] -! CB CA -! CG1 CB -! CG2 CB -! CD CG1 -! N CA -! C CA -! CA HA -! CB HB -! CG1 HG11 -! CG1 HG12 -! CG2 HG21 -! CG2 HG22 -! CG2 HG23 -! CD HD1 -! CD HD2 -! CD HD3 -! O C -! HT1 N -! HT2 N -! HT3 N -! [connections] -! tail C -! [impropers] -! O C CA +N -! [charge_groups] -! N HT1 HT2 HT3 CA HA -! CB HB -! CG2 HG21 HG22 HG23 -! CG1 HG11 HG12 -! CD HD1 HD2 HD3 -! C O -!*------------------------------------------------------------------ -!{NLEU} !charge: 1.0 || LEU N-terminal (standard) -! [atoms] -! 1 N N287 -0.300 -! 2 CA C293 0.250 -! 3 HA H140 0.060 -! 4 CB C136 -0.120 -! 5 HB1 H140 0.060 -! 6 HB2 H140 0.060 -! 7 CG C137 -0.060 -! 8 HG H140 0.060 -! 9 CD1 C135 -0.180 -! 10 HD11 H140 0.060 -! 11 HD12 H140 0.060 -! 12 HD13 H140 0.060 -! 13 CD2 C135 -0.180 -! 14 HD21 H140 0.060 -! 15 HD22 H140 0.060 -! 16 HD23 H140 0.060 -! 17 C C235 0.500 -! 18 O O236 -0.500 -! 19 HT1 H290 0.330 -! 20 HT2 H290 0.330 -! 21 HT3 H290 0.330 -! [bonds] -! CB CA -! CG CB -! CD1 CG -! CD2 CG -! N CA -! C CA -! CA HA -! CB HB1 -! CB HB2 -! CG HG -! CD1 HD11 -! CD1 HD12 -! CD1 HD13 -! CD2 HD21 -! CD2 HD22 -! CD2 HD23 -! O C -! HT1 N -! HT2 N -! HT3 N -! [connections] -! tail C -! [impropers] -! O C CA +N -! [charge_groups] -! N HT1 HT2 HT3 CA HA -! CB HB1 HB2 -! CG HG -! CD1 HD11 HD12 HD13 -! CD2 HD21 HD22 HD23 -! C O -!*------------------------------------------------------------------ -!{NLYS} !charge: 2.0 || LYS N-terminal (standard) -! [atoms] -! 1 N N287 -0.300 -! 2 CA C293 0.250 -! 3 HA H140 0.060 -! 4 CB C136 -0.120 -! 5 HB1 H140 0.060 -! 6 HB2 H140 0.060 -! 7 CG C136 -0.120 -! 8 HG1 H140 0.060 -! 9 HG2 H140 0.060 -! 10 CD C136 -0.120 -! 11 HD1 H140 0.060 -! 12 HD2 H140 0.060 -! 13 CE C292 0.190 -! 14 HE1 H140 0.060 -! 15 HE2 H140 0.060 -! 16 NZ N287 -0.300 -! 17 HZ1 H290 0.330 -! 18 HZ2 H290 0.330 -! 19 HZ3 H290 0.330 -! 20 C C235 0.500 -! 21 O O236 -0.500 -! 22 HT1 H290 0.330 -! 23 HT2 H290 0.330 -! 24 HT3 H290 0.330 -! [bonds] -! CB CA -! CG CB -! CD CG -! CE CD -! NZ CE -! N CA -! C CA -! CA HA -! CB HB1 -! CB HB2 -! CG HG1 -! CG HG2 -! CD HD1 -! CD HD2 -! CE HE1 -! CE HE2 -! O C -! NZ HZ1 -! NZ HZ2 -! NZ HZ3 -! HT1 N -! HT2 N -! HT3 N -! [connections] -! tail C -! [impropers] -! O C CA +N -! [charge_groups] -! N HT1 HT2 HT3 CA HA -! CB HB1 HB2 -! CG HG1 HG2 -! CD HD1 HD2 -! CE HE1 HE2 NZ HZ1 HZ2 HZ3 -! C O -!*------------------------------------------------------------------ -!{NMET} !charge: 1.0 || MET N-terminal (standard) -! [atoms] -! 1 N N287 -0.300 -! 2 CA C293 0.250 -! 3 HA H140 0.060 -! 4 CB C136 -0.120 -! 5 HB1 H140 0.060 -! 6 HB2 H140 0.060 -! 7 CG C210 0.0475 -! 8 HG1 H140 0.060 -! 9 HG2 H140 0.060 -! 10 SD S202 -0.335 -! 11 CE C209 -0.0125 -! 12 HE1 H140 0.060 -! 13 HE2 H140 0.060 -! 14 HE3 H140 0.060 -! 15 C C235 0.500 -! 16 O O236 -0.500 -! 17 HT1 H290 0.330 -! 18 HT2 H290 0.330 -! 19 HT3 H290 0.330 -! [bonds] -! CB CA -! CG CB -! SD CG -! CE SD -! N CA -! C CA -! CA HA -! CB HB1 -! CB HB2 -! CG HG1 -! CG HG2 -! CE HE1 -! CE HE2 -! CE HE3 -! O C -! HT1 N -! HT2 N -! HT3 N -! [connections] -! tail C -! [impropers] -! O C CA +N -! [charge_groups] -! N HT1 HT2 HT3 CA HA -! CB HB1 HB2 -! CG HG1 HG2 SD CE HE1 HE2 HE3 -! C O -!*------------------------------------------------------------------ -!{NPHE} !charge: 1.0 || PHE N-terminal (standard) -! [atoms] -! 1 N N287 -0.300 -! 2 CA C293 0.250 -! 3 HA H140 0.060 -! 4 CB C149 -0.005 -! 5 HB1 H140 0.060 -! 6 HB2 H140 0.060 -! 7 CG C145 -0.115 -! 8 CD1 C145 -0.115 -! 9 HD1 H146 0.115 -! 10 CE1 C145 -0.115 -! 11 HE1 H146 0.115 -! 12 CZ C145 -0.115 -! 13 HZ H146 0.115 -! 14 CD2 C145 -0.115 -! 15 HD2 H146 0.115 -! 16 CE2 C145 -0.115 -! 17 HE2 H146 0.115 -! 18 C C235 0.500 -! 19 O O236 -0.500 -! 20 HT1 H290 0.330 -! 21 HT2 H290 0.330 -! 22 HT3 H290 0.330 -! [bonds] -! CB CA -! CG CB -! CD2 CG -! CE1 CD1 -! CZ CE2 -! N CA -! C CA -! CA HA -! CB HB1 -! CB HB2 -! CD1 HD1 -! CD2 HD2 -! CE1 HE1 -! O C -! CD1 CG -! CZ CE1 -! CE2 CD2 -! CE2 HE2 -! CZ HZ -! HT1 N -! HT2 N -! HT3 N -! [connections] -! tail C -! [impropers] -! O C CA +N -! HD1 CD1 CG CE1 -! HE1 CE1 CD1 CZ -! HZ CZ CE1 CE2 -! CB CG CD1 CD2 -! HD2 CD2 CE2 CG -! HE2 CE2 CZ CD2 -! [charge_groups] -! N HT1 HT2 HT3 CA HA -! CB HB1 HB2 CG -! CD1 HD1 -! CE1 HE1 -! CZ HZ -! CD2 HD2 -! CE2 HE2 -! C O -!*------------------------------------------------------------------ -!{NPRO} !charge: 1.1 || PRO N-terminal (standard) -! [atoms] -! 1 N N287 -0.300 -! 2 CD C245 -0.050 -! 3 HD1 H140 0.060 -! 4 HD2 H140 0.060 -! 5 CA C293 0.250 -! 6 HA H140 0.060 -! 7 CB C136 -0.120 -! 8 HB1 H140 0.060 -! 9 HB2 H140 0.060 -! 10 CG C136 -0.120 -! 11 HG1 H140 0.060 -! 12 HG2 H140 0.060 -! 13 C C235 0.500 -! 14 O O236 -0.500 -! 15 HT1 H290 0.330 -! 16 HT2 H290 0.330 -! [bonds] -! C CA -! N CA -! CA CB -! CB CG -! CG CD -! N CD -! HA CA -! HG1 CG -! HG2 CG -! HD1 CD -! HD2 CD -! HB1 CB -! HB2 CB -! O C -! HT1 N -! HT2 N -! [connections] -! tail C -! [impropers] -! O C CA +N -! [charge_groups] -! N CD HD1 HD2 CA HA HT1 HT2 -! CB HB1 HB2 -! CG HG1 HG2 -! C O -!*------------------------------------------------------------------ -!{NSER} !charge: 1.0 || SER N-terminal (standard) -! [atoms] -! 1 N N287 -0.300 -! 2 CA C293 0.250 -! 3 HA H140 0.060 -! 4 CB C157 0.145 -! 5 HB1 H140 0.060 -! 6 HB2 H140 0.060 -! 7 OG O154 -0.683 -! 8 HG1 H155 0.418 -! 9 C C235 0.500 -! 10 O O236 -0.500 -! 11 HT1 H290 0.330 -! 12 HT2 H290 0.330 -! 13 HT3 H290 0.330 -! [bonds] -! CB CA -! OG CB -! N CA -! C CA -! CA HA -! CB HB1 -! CB HB2 -! OG HG1 -! O C -! HT1 N -! HT2 N -! HT3 N -! [connections] -! tail C -! [impropers] -! O C CA +N -! [charge_groups] -! N HT1 HT2 HT3 CA HA -! CB HB1 HB2 OG HG1 -! C O -!*------------------------------------------------------------------ -!{NTHR} !charge: 1.0 || THR N-terminal (standard) -! [atoms] -! 1 N N287 -0.300 -! 2 CA C293 0.250 -! 3 HA H140 0.060 -! 4 CB C158 0.205 -! 5 HB H140 0.060 -! 6 OG1 O154 -0.683 -! 7 HG1 H155 0.418 -! 8 CG2 C135 -0.180 -! 9 HG21 H140 0.060 -! 10 HG22 H140 0.060 -! 11 HG23 H140 0.060 -! 12 C C235 0.500 -! 13 O O236 -0.500 -! 14 HT1 H290 0.330 -! 15 HT2 H290 0.330 -! 16 HT3 H290 0.330 -! [bonds] -! CB CA -! OG1 CB -! CG2 CB -! N CA -! C CA -! CA HA -! CB HB -! OG1 HG1 -! CG2 HG21 -! CG2 HG22 -! CG2 HG23 -! O C -! HT1 N -! HT2 N -! HT3 N -! [connections] -! tail C -! [impropers] -! O C CA +N -! [charge_groups] -! N HT1 HT2 HT3 CA HA -! CB HB OG1 HG1 -! CG2 HG21 HG22 HG23 -! C O -!*------------------------------------------------------------------ -!{NTRP} !charge: 1.0 || TRP N-terminal (standard) -! [atoms] -! 1 N N287 -0.300 -! 2 CA C293 0.250 -! 3 HA H140 0.060 -! 4 CB C136 -0.120 -! 5 HB1 H140 0.060 -! 6 HB2 H140 0.060 -! 7 CG C500 0.075 -! 8 CD1 C514 -0.115 -! 9 HD1 H146 0.115 -! 10 NE1 N503 -0.570 -! 11 HE1 H504 0.420 -! 12 CE2 C502 0.130 -! 13 CD2 C501 -0.055 -! 14 CE3 C145 -0.115 -! 15 HE3 H146 0.115 -! 16 CZ3 C145 -0.115 -! 17 HZ3 H146 0.115 -! 18 CZ2 C145 -0.115 -! 19 HZ2 H146 0.115 -! 20 CH2 C145 -0.115 -! 21 HH2 H146 0.115 -! 22 C C235 0.500 -! 23 O O236 -0.500 -! 24 HT1 H290 0.330 -! 25 HT2 H290 0.330 -! 26 HT3 H290 0.330 -! [bonds] -! CB CA -! CG CB -! CD2 CG -! NE1 CD1 -! CZ2 CE2 -! N CA -! C CA -! CZ3 CH2 -! CD2 CE3 -! NE1 CE2 -! CA HA -! CB HB1 -! CB HB2 -! CD1 HD1 -! NE1 HE1 -! CE3 HE3 -! CZ2 HZ2 -! CZ3 HZ3 -! CH2 HH2 -! O C -! CD1 CG -! CE2 CD2 -! CZ3 CE3 -! CH2 CZ2 -! HT1 N -! HT2 N -! HT3 N -! [connections] -! tail C -! [impropers] -! O C CA +N -! CB CG CD1 CD2 -! HD1 CD1 CG NE1 -! HE1 NE1 CD1 CE2 -! HZ2 CZ2 CE2 CH2 -! HH2 CH2 CZ2 CZ3 -! HZ3 CZ3 CH2 CE3 -! HE3 CE3 CZ3 CD2 -! CE2 CD2 CE3 CG -! CZ2 CE2 CD2 NE1 -! [charge_groups] -! N HT1 HT2 HT3 CA HA -! CB HB1 HB2 -! CG CD1 HD1 NE1 HE1 CE2 CD2 -! CE3 HE3 -! CZ3 HZ3 -! CZ2 HZ2 -! CH2 HH2 -! C O -!*------------------------------------------------------------------ -!{NTYR} !charge: 1.0 || TYR N-terminal (standard) -! [atoms] -! 1 N N287 -0.300 -! 2 CA C293 0.250 -! 3 HA H140 0.060 -! 4 CB C149 -0.005 -! 5 HB1 H140 0.060 -! 6 HB2 H140 0.060 -! 7 CG C145 -0.115 -! 8 CD1 C145 -0.115 -! 9 HD1 H146 0.115 -! 10 CE1 C145 -0.115 -! 11 HE1 H146 0.115 -! 12 CZ C166 0.150 -! 13 OH O167 -0.585 -! 14 HH H168 0.435 -! 15 CD2 C145 -0.115 -! 16 HD2 H146 0.115 -! 17 CE2 C145 -0.115 -! 18 HE2 H146 0.115 -! 19 C C235 0.500 -! 20 O O236 -0.500 -! 21 HT1 H290 0.330 -! 22 HT2 H290 0.330 -! 23 HT3 H290 0.330 -! [bonds] -! CB CA -! CG CB -! CD2 CG -! CE1 CD1 -! CZ CE2 -! OH CZ -! N CA -! C CA -! CA HA -! CB HB1 -! CB HB2 -! CD1 HD1 -! CD2 HD2 -! CE1 HE1 -! CE2 HE2 -! OH HH -! O C -! CD1 CG -! CE1 CZ -! CE2 CD2 -! HT1 N -! HT2 N -! HT3 N -! [connections] -! tail C -! [impropers] -! O C CA +N -! HD1 CD1 CG CE1 -! HE1 CE1 CD1 CZ -! OH CZ CE1 CE2 -! CB CG CD1 CD2 -! HD2 CD2 CE2 CG -! HE2 CE2 CZ CD2 -! [charge_groups] -! N HT1 HT2 HT3 CA HA -! CB HB1 HB2 CG -! CD1 HD1 -! CE1 HE1 -! CZ OH HH -! CD2 HD2 -! CE2 HE2 -! C O -!*------------------------------------------------------------------ -!{NVAL} !charge: 1.0 || VAL N-terminal (standard) -! [atoms] -! 1 N N287 -0.300 -! 2 CA C293 0.250 -! 3 HA H140 0.060 -! 4 CB C137 -0.060 -! 5 HB H140 0.060 -! 6 CG1 C135 -0.180 -! 7 HG11 H140 0.060 -! 8 HG12 H140 0.060 -! 9 HG13 H140 0.060 -! 10 CG2 C135 -0.180 -! 11 HG21 H140 0.060 -! 12 HG22 H140 0.060 -! 13 HG23 H140 0.060 -! 14 C C235 0.500 -! 15 O O236 -0.500 -! 16 HT1 H290 0.330 -! 17 HT2 H290 0.330 -! 18 HT3 H290 0.330 -! [bonds] -! CB CA -! CG1 CB -! CG2 CB -! N CA -! C CA -! CA HA -! CB HB -! CG1 HG11 -! CG1 HG12 -! CG1 HG13 -! CG2 HG21 -! CG2 HG22 -! CG2 HG23 -! O C -! HT1 N -! HT2 N -! HT3 N -! [connections] -! tail C -! [impropers] -! O C CA +N -! [charge_groups] -! N HT1 HT2 HT3 CA HA -! CB HB -! CG1 HG11 HG12 HG13 -! CG2 HG21 HG22 HG23 -! C O -*------------------------------------------------------------------ {PHE} !charge: 0.00 || [atoms] 1 N N238 -0.500 @@ -3672,7 +1298,8 @@ {HOH} !charge: 0.000 || tip3p water model, generate using noangle nodihedral [info] solvent 1 - density 0.0335 + density 0.0335 + epsilon 80100 [atoms] 1 O OT -0.834 2 H1 HT 0.417 @@ -3875,4 +1502,46 @@ CG2 HG21 HG22 HG23 C O *------------------------------------------------------------------ - +{NME} !charge 0.0, methyl cap, types and charges from original ff file + [atoms] + 1 N N238 -0.500 + 2 H H241 0.300 + 3 CH3 C242 0.020 + 4 H31 H140 0.060 + 5 H32 H140 0.060 + 6 H33 H140 0.060 + [bonds] + N H + N CH3 + CH3 H31 + CH3 H32 + CH3 H33 + [impropers] + -C N CH3 H + [connections] + head N + [charge_groups] + N H CH3 H31 H32 H33 +*------------------------------------------------------------------ +{ACE} !charge 0.0, acetyl cap, types and charges from original ff file + [atoms] + 1 H31 H140 0.060 + 2 CH3 C135 -0.180 + 3 H32 H140 0.060 + 4 H33 H140 0.060 + 5 C C235 0.500 + 6 O O236 -0.500 + [bonds] + CH3 H31 + CH3 H32 + CH3 H33 + CH3 C + C O + [impropers] + CH3 C +N O + [connections] + tail C + [charge_groups] + CH3 H31 H32 H33 + C O +*--------------------------------------------------------------------- diff --git a/ff/oplsaam2015/qoplsaa.prm b/ff/oplsaam2015/qoplsaa.prm index 295d11e..551537b 100644 --- a/ff/oplsaam2015/qoplsaa.prm +++ b/ff/oplsaam2015/qoplsaa.prm @@ -2196,50 +2196,61 @@ C267 C136 C283 C271 0.299 -1.000 0.000 1 C267 C136 C283 C271 0.779 -2.000 180.000 1 C267 C136 C283 C271 0.128 3.000 0.000 1 ! from here manually added by Paul Bauer 06.10.2015 from FFLD 14 -C135 C944 N943 C942 0.914 -1 0 1 -C135 C944 N943 C942 0.122 -2 180 1 -C135 C944 N943 C942 -0.249 3 0 1 -H140 C944 N943 C942 0.089 3 0 1 -C944 N943 C942 N940 3.968 2 180 1 -C944 N943 C942 N941 3.968 2 180 1 -H240 N943 C942 N940 1 2 180 1 -H240 N943 C942 N941 1 2 180 1 -N943 C942 N940 H240 1 2 180 1 -N941 C942 N940 H240 1 2 180 1 -N943 C942 N940 H240 4 2 180 1 -N940 C942 N940 H240 4 2 180 1 -C224 C136 C136 C944 0.65 -1 0 1 -C224 C136 C136 C944 -0.025 -2 180 1 -C224 C136 C136 C944 0.1 3 0 1 -H140 C136 C136 C944 0.15 3 0 1 -C136 C136 C944 N943 1.366 -1 0 1 -C136 C136 C944 N943 -0.115 -2 180 1 -C136 C136 C944 N943 0.243 3 0 1 -C136 C136 C944 H140 0.15 3 0 1 -H140 C136 C944 N943 -0.291 3 0 1 -H140 C136 C944 H140 0.15 3 0 1 -C136 C944 N943 C942 0.914 -1 0 1 -C136 C944 N943 C942 0.122 -2 180 1 -C136 C944 N943 C942 -0.249 3 0 1 -C136 C944 N943 H240 -0.095 -1 0 1 -C136 C944 N943 H240 -0.208 -2 180 1 -C136 C944 N943 H240 0.209 3 0 1 -H140 C944 N943 C942 0.089 3 0 1 -H140 C944 N943 H240 0 3 0 1 -C944 N943 C942 N940 3.968 2 180 1 -C944 N943 C942 N941 3.968 2 180 1 -C136 C136 C292 N900 1.196 -1 0 1 -C136 C136 C292 N900 -0.337 -2 180 1 -C136 C136 C292 N900 0.275 3 0 1 -H140 C136 C292 N900 -0.507 -1 0 1 -H140 C136 C292 N900 -0.354 -2 180 1 -H140 C136 C292 N900 0.236 3 0 1 -C136 C292 N900 H240 -0.095 -1 0 1 -C136 C292 N900 H240 -0.208 -2 180 1 -C136 C292 N900 H240 0.209 3 0 1 -H140 C292 N900 H240 0.2 3 0 1 -N943 C942 N941 H240 4.0 2 180 1 -N940 C942 N941 H240 4.0 2 180 1 +! updated on 27.06.2017 -> new paramteres from maestro/2014 ffld_server -version 14 +C942 N943 C944 C136 -0.249 -3.0 0.0 1.0 # FFLD: high 0 CT-CT-NY-CD ==> CD-NY-CT-CT +C942 N943 C944 C136 0.1215 -2.0 180.0 1.0 # FFLD: high 0 CT-CT-NY-CD ==> CD-NY-CT-CT +C942 N943 C944 C136 0.9145 1.0 0.0 1.0 # FFLD: high 0 CT-CT-NY-CD ==> CD-NY-CT-CT +C942 N943 C944 H140 0.0885 3.0 0.0 1.0 # FFLD: high 0 HC-CT-NY-CD ==> CD-NY-CT-HC +C224 C136 C136 C944 0.1 -3.0 0.0 1.0 # FFLD: high 0 CT1-CTN-CT-CT ==> CT-CT-CTN-CT1 +C224 C136 C136 C944 -0.025 -2.0 180.0 1.0 # FFLD: high 0 CT1-CTN-CT-CT ==> CT-CT-CTN-CT1 +C224 C136 C136 C944 0.65 1.0 0.0 1.0 # FFLD: high 0 CT1-CTN-CT-CT ==> CT-CT-CTN-CT1 +C136 C136 C944 H140 0.15 3.0 0.0 1.0 # FFLD: high 0 CTN-CT-CT-HC ==> CTN-CT-CT-HC +C136 C136 C944 N943 0.2425 -3.0 0.0 1.0 # FFLD: high 0 CTN-CT-CT-NY ==> CTN-CT-CT-NY +C136 C136 C944 N943 -0.1145 -2.0 180.0 1.0 # FFLD: high 0 CTN-CT-CT-NY ==> CTN-CT-CT-NY +C136 C136 C944 N943 1.366 1.0 0.0 1.0 # FFLD: high 0 CTN-CT-CT-NY ==> CTN-CT-CT-NY +C136 C944 N943 H240 0.209 -3.0 0.0 1.0 # FFLD: high 0 CT-CT-NY-H ==> CT-CT-NY-H +C136 C944 N943 H240 -0.2085 -2.0 180.0 1.0 # FFLD: high 0 CT-CT-NY-H ==> CT-CT-NY-H +C136 C944 N943 H240 -0.095 1.0 0.0 1.0 # FFLD: high 0 CT-CT-NY-H ==> CT-CT-NY-H +C944 C136 C136 H140 0.15 3.0 0.0 1.0 # FFLD: high 0 HC-CTN-CT-CT ==> CT-CT-CTN-HC +C944 N943 C942 N940 -3.5085 -3.0 0.0 1.0 # FFLD: high 0 CT-NY-CD-NI ==> CT-NY-CD-NI +C944 N943 C942 N940 -0.491 -2.0 180.0 1.0 # FFLD: high 0 CT-NY-CD-NI ==> CT-NY-CD-NI +C944 N943 C942 N940 4.524 1.0 0.0 1.0 # FFLD: high 0 CT-NY-CD-NI ==> CT-NY-CD-NI +C944 N943 C942 N941 -3.5085 -3.0 0.0 1.0 # FFLD: high 0 CT-NY-CD-NY ==> CT-NY-CD-NY +C944 N943 C942 N941 -0.491 -2.0 180.0 1.0 # FFLD: high 0 CT-NY-CD-NY ==> CT-NY-CD-NY +C944 N943 C942 N941 4.524 1.0 0.0 1.0 # FFLD: high 0 CT-NY-CD-NY ==> CT-NY-CD-NY +H140 C136 C944 H140 0.15 3.0 0.0 1.0 # FFLD: high 0 HC-CT-CT-HC ==> HC-CT-CT-HC +H140 C136 C944 N943 -0.291 3.0 0.0 1.0 # FFLD: high 0 HC-CT-CT-NY ==> HC-CT-CT-NY +H140 C944 N943 H240 0.0 1.0 0.0 1.0 # FFLD: high 0 HC-CT-NY-H ==> H-NY-CT-HC +H240 N940 C942 N941 0.209 -3.0 0.0 1.0 # FFLD: high 0 NY-CD-NI-H ==> H-NI-CD-NY +H240 N940 C942 N941 -0.2085 -2.0 180.0 1.0 # FFLD: high 0 NY-CD-NI-H ==> H-NI-CD-NY +H240 N940 C942 N941 -2.345 1.0 0.0 1.0 # FFLD: high 0 NY-CD-NI-H ==> H-NI-CD-NY +H240 N940 C942 N943 0.209 -3.0 0.0 1.0 # FFLD: high 0 NY-CD-NI-H ==> H-NI-CD-NY +H240 N940 C942 N943 -0.2085 -2.0 180.0 1.0 # FFLD: high 0 NY-CD-NI-H ==> H-NI-CD-NY +H240 N940 C942 N943 -2.345 1.0 0.0 1.0 # FFLD: high 0 NY-CD-NI-H ==> H-NI-CD-NY +H240 N941 C942 N940 0.209 -3.0 0.0 1.0 # FFLD: high 0 NI-CD-NY-H ==> H-NY-CD-NI +H240 N941 C942 N940 -0.2085 -2.0 180.0 1.0 # FFLD: high 0 NI-CD-NY-H ==> H-NY-CD-NI +H240 N941 C942 N940 -0.095 1.0 0.0 1.0 # FFLD: high 0 NI-CD-NY-H ==> H-NY-CD-NI +H240 N941 C942 N943 0.209 -3.0 0.0 1.0 # FFLD: high 0 NY-CD-NY-H ==> H-NY-CD-NY +H240 N941 C942 N943 -0.2085 -2.0 180.0 1.0 # FFLD: high 0 NY-CD-NY-H ==> H-NY-CD-NY +H240 N941 C942 N943 -0.095 1.0 0.0 1.0 # FFLD: high 0 NY-CD-NY-H ==> H-NY-CD-NY +H240 N943 C942 N940 0.209 -3.0 0.0 1.0 # FFLD: high 0 H-NY-CD-NI ==> H-NY-CD-NI +H240 N943 C942 N940 -0.2085 -2.0 180.0 1.0 # FFLD: high 0 H-NY-CD-NI ==> H-NY-CD-NI +H240 N943 C942 N940 -0.095 1.0 0.0 1.0 # FFLD: high 0 H-NY-CD-NI ==> H-NY-CD-NI +H240 N943 C942 N941 0.209 -3.0 0.0 1.0 # FFLD: high 0 H-NY-CD-NY ==> H-NY-CD-NY +H240 N943 C942 N941 -0.2085 -2.0 180.0 1.0 # FFLD: high 0 H-NY-CD-NY ==> H-NY-CD-NY +H240 N943 C942 N941 -0.095 1.0 0.0 1.0 # FFLD: high 0 H-NY-CD-NY ==> H-NY-CD-NY +! also new LYN parameters +C136 C136 C292 N900 1.497 -3.0 0.0 1.0 # FFLD: high 0 CT-CT-CT-NT ==> CT-CT-CT-NT +C136 C136 C292 N900 0.0345 -2.0 180.0 1.0 # FFLD: high 0 CT-CT-CT-NT ==> CT-CT-CT-NT +C136 C136 C292 N900 -2.5 1.0 0.0 1.0 # FFLD: high 0 CT-CT-CT-NT ==> CT-CT-CT-NT +C136 C292 N900 H240 0.209 -3.0 0.0 1.0 # FFLD: high 0 CT-CT-NT-H ==> CT-CT-NT-H +C136 C292 N900 H240 -0.2085 -2.0 180.0 1.0 # FFLD: high 0 CT-CT-NT-H ==> CT-CT-NT-H +C136 C292 N900 H240 -0.095 1.0 0.0 1.0 # FFLD: high 0 CT-CT-NT-H ==> CT-CT-NT-H + +H140 C136 C292 N900 0.2365 -3.0 0.0 1.0 # FFLD: high 0 HC-CT-CT-NT ==> HC-CT-CT-NT +H140 C136 C292 N900 -0.3545 -2.0 180.0 1.0 # FFLD: high 0 HC-CT-CT-NT ==> HC-CT-CT-NT +H140 C136 C292 N900 -0.5065 1.0 0.0 1.0 # FFLD: high 0 HC-CT-CT-NT ==> HC-CT-CT-NT +H140 C292 N900 H240 0.2 3.0 0.0 1.0 # FFLD: high 0 HC-CT-NT-H ==> H-NT-CT-HC [impropers] *iaci iacj iack iacl forceK imp0