-C N
[ impropers ]
CA +N C O
- -C CD N CA
+ -C CD N CA
[ HYP ] ; S Park, R J Radmer, T E Klein & V S Pande (submitted).
[ atoms ]
[ CALA ]
[ atoms ]
- N N -0.38210 1
- H H 0.26810 2
- CA CT -0.17470 3
- HA H1 0.10670 4
- CB CT -0.20930 5
- HB1 HC 0.07640 6
- HB2 HC 0.07640 7
- HB3 HC 0.07640 8
- C C 0.77310 9
- OC1 O2 -0.80550 10
- OC2 O2 -0.80550 11
+ N N -0.622202 1
+ H H 0.359784 2
+ CA CT -0.054102 3
+ HA H1 0.123283 4
+ CB CT -0.185718 5
+ HB1 HC 0.069652 6
+ HB2 HC 0.069652 7
+ HB3 HC 0.069652 8
+ C C 0.664014 9
+ OC1 O2 -0.747007 10
+ OC2 O2 -0.747007 11
[ bonds ]
N H
N CA
[ CGLY ]
[ atoms ]
- N N -0.38210 1
- H H 0.26810 2
- CA CT -0.24930 3
- HA1 H1 0.10560 4
- HA2 H1 0.10560 5
- C C 0.72310 6
- OC1 O2 -0.78550 7
- OC2 O2 -0.78550 8
+ N N -0.523362 1
+ H H 0.349622 2
+ CA CT -0.316659 3
+ HA1 H1 0.160200 4
+ HA2 H1 0.160200 5
+ C C 0.661797 6
+ OC1 O2 -0.745899 7
+ OC2 O2 -0.745899 8
[ bonds ]
N H
N CA
[ CSER ]
[ atoms ]
- N N -0.38210 1
- H H 0.26810 2
- CA CT -0.27220 3
- HA H1 0.13040 4
- CB CT 0.11230 5
- HB1 H1 0.08130 6
- HB2 H1 0.08130 7
- OG OH -0.65140 8
- HG HO 0.44740 9
- C C 0.81130 10
- OC1 O2 -0.81320 11
- OC2 O2 -0.81320 12
+ N N -0.676281 1
+ H H 0.369239 2
+ CA CT -0.072385 3
+ HA H1 0.158185 4
+ CB CT 0.132964 5
+ HB1 H1 0.048008 6
+ HB2 H1 0.048008 7
+ OG OH -0.580479 8
+ HG HO 0.402742 9
+ C C 0.594367 10
+ OC1 O2 -0.712184 11
+ OC2 O2 -0.712184 12
[ bonds ]
N H
N CA
[ CTHR ]
[ atoms ]
- N N -0.38210 1
- H H 0.26810 2
- CA CT -0.24200 3
- HA H1 0.12070 4
- CB CT 0.30250 5
- HB H1 0.00780 6
- CG2 CT -0.18530 7
- HG21 HC 0.05860 8
- HG22 HC 0.05860 9
- HG23 HC 0.05860 10
- OG1 OH -0.64960 11
- HG1 HO 0.41190 12
- C C 0.78100 13
- OC1 O2 -0.80440 14
- OC2 O2 -0.80440 15
+ N N -0.351668 1
+ H H 0.299320 2
+ CA CT -0.500569 3
+ HA H1 0.237658 4
+ CB CT 0.294422 5
+ HB H1 0.031148 6
+ CG2 CT -0.137163 7
+ HG21 HC 0.051258 8
+ HG22 HC 0.051258 9
+ HG23 HC 0.051258 10
+ OG1 OH -0.605568 11
+ HG1 HO 0.408646 12
+ C C 0.681669 13
+ OC1 O2 -0.755835 14
+ OC2 O2 -0.755835 15
[ bonds ]
N H
N CA
[ CLEU ]
[ atoms ]
- N N -0.38210 1
- H H 0.26810 2
- CA CT -0.28470 3
- HA H1 0.13460 4
- CB CT -0.24690 5
- HB1 HC 0.09740 6
- HB2 HC 0.09740 7
- CG CT 0.37060 8
- HG HC -0.03740 9
- CD1 CT -0.41630 10
- HD11 HC 0.10380 11
- HD12 HC 0.10380 12
- HD13 HC 0.10380 13
- CD2 CT -0.41630 14
- HD21 HC 0.10380 15
- HD22 HC 0.10380 16
- HD23 HC 0.10380 17
- C C 0.83260 18
- OC1 O2 -0.81990 19
- OC2 O2 -0.81990 20
- [ bonds ]
- N H
+ N N -0.556595 1
+ H H 0.338672 2
+ CA CT -0.229880 3
+ HA H1 0.190710 4
+ CB CT -0.102213 5
+ HB1 HC 0.054816 6
+ HB2 HC 0.054816 7
+ CG CT 0.195714 8
+ HG HC 0.005286 9
+ CD1 CT -0.136225 10
+ HD11 HC 0.025188 11
+ HD12 HC 0.025188 12
+ HD13 HC 0.025188 13
+ CD2 CT -0.136225 14
+ HD21 HC 0.025188 15
+ HD22 HC 0.025188 16
+ HD23 HC 0.025188 17
+ C C 0.598427 18
+ OC1 O2 -0.714214 19
+ OC2 O2 -0.714214 20
+ [ bonds ]
+ N H
N CA
CA HA
CA CB
[ CILE ]
[ atoms ]
- N N -0.38210 1
- H H 0.26810 2
- CA CT -0.31000 3
- HA H1 0.13750 4
- CB CT 0.03630 5
- HB HC 0.07660 6
- CG2 CT -0.34980 7
- HG21 HC 0.10210 8
- HG22 HC 0.10210 9
- HG23 HC 0.10210 10
- CG1 CT -0.03230 11
- HG11 HC 0.03210 12
- HG12 HC 0.03210 13
- CD CT -0.06990 14
- HD1 HC 0.01960 15
- HD2 HC 0.01960 16
- HD3 HC 0.01960 17
- C C 0.83430 18
- OC1 O2 -0.81900 19
- OC2 O2 -0.81900 20
+ N N -0.509270 1
+ H H 0.314575 2
+ CA CT -0.227333 3
+ HA H1 0.143304 4
+ CB CT 0.044365 5
+ HB HC 0.064001 6
+ CG2 CT -0.162378 7
+ HG21 HC 0.040070 8
+ HG22 HC 0.040070 9
+ HG23 HC 0.040070 10
+ CG1 CT 0.058658 11
+ HG11 HC 0.008847 12
+ HG12 HC 0.008847 13
+ CD CT -0.101376 14
+ HD1 HC 0.022516 15
+ HD2 HC 0.022516 16
+ HD3 HC 0.022516 17
+ C C 0.671034 18
+ OC1 O2 -0.750517 19
+ OC2 O2 -0.750517 20
[ bonds ]
N H
N CA
[ CVAL ]
[ atoms ]
- N N -0.38210 1
- H H 0.26810 2
- CA CT -0.34380 3
- HA H1 0.14380 4
- CB CT 0.19400 5
- HB HC 0.03080 6
- CG1 CT -0.30640 7
- HG11 HC 0.08360 8
- HG12 HC 0.08360 9
- HG13 HC 0.08360 10
- CG2 CT -0.30640 11
- HG21 HC 0.08360 12
- HG22 HC 0.08360 13
- HG23 HC 0.08360 14
- C C 0.83500 15
- OC1 O2 -0.81730 16
- OC2 O2 -0.81730 17
+ N N -0.217054 1
+ H H 0.243122 2
+ CA CT -0.374120 3
+ HA H1 0.097720 4
+ CB CT 0.202309 5
+ HB HC -0.022953 6
+ CG1 CT -0.137796 7
+ HG11 HC 0.029428 8
+ HG12 HC 0.029428 9
+ HG13 HC 0.029428 10
+ CG2 CT -0.137796 11
+ HG21 HC 0.029428 12
+ HG22 HC 0.029428 13
+ HG23 HC 0.029428 14
+ C C 0.525616 15
+ OC1 O2 -0.677808 16
+ OC2 O2 -0.677808 17
[ bonds ]
N H
N CA
[ CASN ]
[ atoms ]
- N N -0.38210 1
- H H 0.26810 2
- CA CT -0.20800 3
- HA H1 0.13580 4
- CB CT -0.22990 5
- HB1 HC 0.10230 6
- HB2 HC 0.10230 7
- CG C 0.71530 8
- OD1 O -0.60100 9
- ND2 N -0.90840 10
- HD21 H 0.41500 11
- HD22 H 0.41500 12
- C C 0.80500 13
- OC1 O2 -0.81470 14
- OC2 O2 -0.81470 15
+ N N -0.626530 1
+ H H 0.343242 2
+ CA CT 0.014405 3
+ HA H1 0.085796 4
+ CB CT -0.029468 5
+ HB1 HC 0.045738 6
+ HB2 HC 0.045738 7
+ CG C 0.551512 8
+ OD1 O -0.567440 9
+ ND2 N -0.766241 10
+ HD21 H 0.366624 11
+ HD22 H 0.366624 12
+ C C 0.607381 13
+ OC1 O2 -0.718691 14
+ OC2 O2 -0.718691 15
[ bonds ]
N H
N CA
[ CGLN ]
[ atoms ]
- N N -0.38210 1
- H H 0.26810 2
- CA CT -0.22480 3
- HA H1 0.12320 4
- CB CT -0.06640 5
- HB1 HC 0.04520 6
- HB2 HC 0.04520 7
- CG CT -0.02100 8
- HG1 HC 0.02030 9
- HG2 HC 0.02030 10
- CD C 0.70930 11
- OE1 O -0.60980 12
- NE2 N -0.95740 13
- HE21 H 0.43040 14
- HE22 H 0.43040 15
- C C 0.77750 16
- OC1 O2 -0.80420 17
- OC2 O2 -0.80420 18
+ N N -0.515135 1
+ H H 0.324299 2
+ CA CT -0.235630 3
+ HA H1 0.164628 4
+ CB CT 0.004813 5
+ HB1 HC 0.030788 6
+ HB2 HC 0.030788 7
+ CG CT -0.024848 8
+ HG1 HC 0.034840 9
+ HG2 HC 0.034840 10
+ CD C 0.662321 11
+ OE1 O -0.588799 12
+ NE2 N -0.883570 13
+ HE21 H 0.395334 14
+ HE22 H 0.395334 15
+ C C 0.600448 16
+ OC1 O2 -0.715224 17
+ OC2 O2 -0.715224 18
[ bonds ]
N H
N CA
[ CARG ]
[ atoms ]
- N N -0.34810 1
- H H 0.27640 2
- CA CT -0.30680 3
- HA H1 0.14470 4
- CB CT -0.03740 5
- HB1 HC 0.03710 6
- HB2 HC 0.03710 7
- CG CT 0.07440 8
- HG1 HC 0.01850 9
- HG2 HC 0.01850 10
- CD CT 0.11140 11
- HD1 H1 0.04680 12
- HD2 H1 0.04680 13
- NE N2 -0.55640 14
- HE H 0.34790 15
- CZ CA 0.83680 16
- NH1 N2 -0.87370 17
- HH11 H 0.44930 18
- HH12 H 0.44930 19
- NH2 N2 -0.87370 20
- HH21 H 0.44930 21
- HH22 H 0.44930 22
- C C 0.85570 23
- OC1 O2 -0.82660 24
- OC2 O2 -0.82660 25
+ N N -0.495340 1
+ H H 0.313864 2
+ CA CT -0.122265 3
+ HA H1 0.093073 4
+ CB CT 0.015820 5
+ HB1 HC 0.040376 6
+ HB2 HC 0.040376 7
+ CG CT 0.013697 8
+ HG1 HC -0.001366 9
+ HG2 HC -0.001366 10
+ CD CT 0.183324 11
+ HD1 H1 0.048691 12
+ HD2 H1 0.048691 13
+ NE N2 -0.468682 14
+ HE H 0.343094 15
+ CZ CA 0.577784 16
+ NH1 N2 -0.712318 17
+ HH11 H 0.406216 18
+ HH12 H 0.406216 19
+ NH2 N2 -0.712318 20
+ HH21 H 0.406216 21
+ HH22 H 0.406216 22
+ C C 0.648763 23
+ OC1 O2 -0.739382 24
+ OC2 O2 -0.739382 25
[ bonds ]
N H
N CA
[ CHID ]
[ atoms ]
- N N -0.38210 1
- H H 0.26810 2
- CA CT -0.17390 3
- HA H1 0.11000 4
- CB CT -0.10460 5
- HB1 HC 0.05650 6
- HB2 HC 0.05650 7
- CG CC 0.02930 8
- ND1 NA -0.38920 9
- HD1 H 0.37550 10
- CE1 CR 0.19250 11
- HE1 H5 0.14180 12
- NE2 NB -0.56290 13
- CD2 CV 0.10010 14
- HD2 H4 0.12410 15
- C C 0.76150 16
- OC1 O2 -0.80160 17
- OC2 O2 -0.80160 18
+ N N -0.692510 1
+ H H 0.357784 2
+ CA CT 0.113471 3
+ HA H1 0.070490 4
+ CB CT -0.032237 5
+ HB1 HC 0.047858 6
+ HB2 HC 0.047858 7
+ CG CC -0.034691 8
+ ND1 NA -0.218767 9
+ HD1 H 0.294104 10
+ CE1 CR 0.152151 11
+ HE1 H5 0.108726 12
+ NE2 NB -0.552887 13
+ CD2 CV 0.073505 14
+ HD2 H4 0.095147 15
+ C C 0.622331 16
+ OC1 O2 -0.726166 17
+ OC2 O2 -0.726166 18
[ bonds ]
N H
N CA
[ CHIE ]
[ atoms ]
- N N -0.38210 1
- H H 0.26810 2
- CA CT -0.26990 3
- HA H1 0.16500 4
- CB CT -0.10680 5
- HB1 HC 0.06200 6
- HB2 HC 0.06200 7
- CG CC 0.27240 8
- ND1 NB -0.55170 9
- CE1 CR 0.15580 10
- HE1 H5 0.14480 11
- NE2 NA -0.26700 12
- HE2 H 0.33190 13
- CD2 CW -0.25880 14
- HD2 H4 0.19570 15
- C C 0.79160 16
- OC1 O2 -0.80650 17
- OC2 O2 -0.80650 18
+ N N -0.678107 1
+ H H 0.378617 2
+ CA CT -0.045762 3
+ HA H1 0.135589 4
+ CB CT -0.088284 5
+ HB1 HC 0.068197 6
+ HB2 HC 0.068197 7
+ CG CC 0.197858 8
+ ND1 NB -0.476371 9
+ CE1 CR 0.048815 10
+ HE1 H5 0.126861 11
+ NE2 NA -0.084778 12
+ HE2 H 0.280364 13
+ CD2 CW -0.254856 14
+ HD2 H4 0.153659 15
+ C C 0.585209 16
+ OC1 O2 -0.707605 17
+ OC2 O2 -0.707605 18
[ bonds ]
N H
N CA
[ CHIP ]
[ atoms ]
- N N -0.34810 1
- H H 0.27640 2
- CA CT -0.14450 3
- HA H1 0.11150 4
- CB CT -0.08000 5
- HB1 HC 0.08680 6
- HB2 HC 0.08680 7
- CG CC 0.02980 8
- ND1 NA -0.15010 9
- HD1 H 0.38830 10
- CE1 CR -0.02510 11
- HE1 H5 0.26940 12
- NE2 NA -0.16830 13
- HE2 H 0.39130 14
- CD2 CW -0.12560 15
- HD2 H4 0.23360 16
- C C 0.80320 17
- OC1 O2 -0.81770 18
- OC2 O2 -0.81770 19
+ N N -0.464193 1
+ H H 0.315351 2
+ CA CT -0.076871 3
+ HA H1 0.125219 4
+ CB CT -0.062807 5
+ HB1 HC 0.092794 6
+ HB2 HC 0.092794 7
+ CG CC 0.057843 8
+ ND1 NA -0.015072 9
+ HD1 H 0.276076 10
+ CE1 CR -0.033413 11
+ HE1 H5 0.226049 12
+ NE2 NA -0.129808 13
+ HE2 H 0.369253 14
+ CD2 CW -0.163636 15
+ HD2 H4 0.220420 16
+ C C 0.513757 17
+ OC1 O2 -0.671879 18
+ OC2 O2 -0.671879 19
[ bonds ]
N H
N CA
[ CTRP ]
[ atoms ]
- N N -0.38210 1
- H H 0.26810 2
- CA CT -0.20840 3
- HA H1 0.12720 4
- CB CT -0.07420 5
- HB1 HC 0.04970 6
- HB2 HC 0.04970 7
- CG C* -0.07960 8
- CD1 CW -0.18080 9
- HD1 H4 0.20430 10
- NE1 NA -0.33160 11
- HE1 H 0.34130 12
- CE2 CN 0.12220 13
- CZ2 CA -0.25940 14
- HZ2 HA 0.15670 15
- CH2 CA -0.10200 16
- HH2 HA 0.14010 17
- CZ3 CA -0.22870 18
- HZ3 HA 0.15070 19
- CE3 CA -0.18370 20
- HE3 HA 0.14910 21
- CD2 CB 0.10780 22
- C C 0.76580 23
- OC1 O2 -0.80110 24
- OC2 O2 -0.80110 25
+ N N -0.629974 1
+ H H 0.341228 2
+ CA CT -0.044250 3
+ HA H1 0.128436 4
+ CB CT -0.058372 5
+ HB1 HC 0.069590 6
+ HB2 HC 0.069590 7
+ CG C* -0.146344 8
+ CD1 CW -0.168076 9
+ HD1 H4 0.178686 10
+ NE1 NA -0.301970 11
+ HE1 H 0.344032 12
+ CE2 CN 0.143447 13
+ CZ2 CA -0.223194 14
+ HZ2 HA 0.136724 15
+ CH2 CA -0.137673 16
+ HH2 HA 0.122474 17
+ CZ3 CA -0.173223 18
+ HZ3 HA 0.121634 19
+ CE3 CA -0.187847 20
+ HE3 HA 0.143053 21
+ CD2 CB 0.102028 22
+ C C 0.615569 23
+ OC1 O2 -0.722785 24
+ OC2 O2 -0.722785 25
[ bonds ]
N H
N CA
[ CPHE ]
[ atoms ]
- N N -0.38210 1
- H H 0.26810 2
- CA CT -0.18250 3
- HA H1 0.10980 4
- CB CT -0.09590 5
- HB1 HC 0.04430 6
- HB2 HC 0.04430 7
- CG CA 0.05520 8
- CD1 CA -0.13000 9
- HD1 HA 0.14080 10
- CE1 CA -0.18470 11
- HE1 HA 0.14610 12
- CZ CA -0.09440 13
- HZ HA 0.12800 14
- CE2 CA -0.18470 15
- HE2 HA 0.14610 16
- CD2 CA -0.13000 17
- HD2 HA 0.14080 18
- C C 0.76600 19
- OC1 O2 -0.80260 20
- OC2 O2 -0.80260 21
+ N N -0.625562 1
+ H H 0.349898 2
+ CA CT -0.088182 3
+ HA H1 0.134954 4
+ CB CT -0.057583 5
+ HB1 HC 0.064041 6
+ HB2 HC 0.064041 7
+ CG CA 0.007991 8
+ CD1 CA -0.098964 9
+ HD1 HA 0.112120 10
+ CE1 CA -0.161136 11
+ HE1 HA 0.128127 12
+ CZ CA -0.097375 13
+ HZ HA 0.117481 14
+ CE2 CA -0.161136 15
+ HE2 HA 0.128127 16
+ CD2 CA -0.098964 17
+ HD2 HA 0.112120 18
+ C C 0.595519 19
+ OC1 O2 -0.712760 20
+ OC2 O2 -0.712760 21
[ bonds ]
N H
N CA
[ CTYR ]
[ atoms ]
- N N -0.38210 1
- H H 0.26810 2
- CA CT -0.20150 3
- HA H1 0.10920 4
- CB CT -0.07520 5
- HB1 HC 0.04900 6
- HB2 HC 0.04900 7
- CG CA 0.02430 8
- CD1 CA -0.19220 9
- HD1 HA 0.17800 10
- CE1 CA -0.24580 11
- HE1 HA 0.16730 12
- CZ C 0.33950 13
- OH OH -0.56430 14
- HH HO 0.40170 15
- CE2 CA -0.24580 16
- HE2 HA 0.16730 17
- CD2 CA -0.19220 18
- HD2 HA 0.17800 19
- C C 0.78170 20
- OC1 O2 -0.80700 21
- OC2 O2 -0.80700 22
+ N N -0.675628 1
+ H H 0.350448 2
+ CA CT -0.012728 3
+ HA H1 0.146871 4
+ CB CT -0.058078 5
+ HB1 HC 0.016619 6
+ HB2 HC 0.016619 7
+ CG CA 0.133018 8
+ CD1 CA -0.194675 9
+ HD1 HA 0.149917 10
+ CE1 CA -0.218820 11
+ HE1 HA 0.148692 12
+ CZ C 0.247734 13
+ OH OH -0.475120 14
+ HH HO 0.370016 15
+ CE2 CA -0.218820 16
+ HE2 HA 0.148692 17
+ CD2 CA -0.194675 18
+ HD2 HA 0.149917 19
+ C C 0.665555 20
+ OC1 O2 -0.747778 21
+ OC2 O2 -0.747778 22
[ bonds ]
N H
N CA
[ CGLU ]
[ atoms ]
- N N -0.51920 1
- H H 0.30550 2
- CA CT -0.20590 3
- HA H1 0.13990 4
- CB CT 0.00710 5
- HB1 HC -0.00780 6
- HB2 HC -0.00780 7
- CG CT 0.06750 8
- HG1 HC -0.05480 9
- HG2 HC -0.05480 10
- CD C 0.81830 11
- OE1 O2 -0.82200 12
- OE2 O2 -0.82200 13
- C C 0.74200 14
- OC1 O2 -0.79300 15
- OC2 O2 -0.79300 16
+ N N -0.748778 1
+ H H 0.396125 2
+ CA CT -0.133159 3
+ HA H1 0.105730 4
+ CB CT 0.185749 5
+ HB1 HC -0.045957 6
+ HB2 HC -0.045957 7
+ CG CT -0.033125 8
+ HG1 HC -0.011832 9
+ HG2 HC -0.011832 10
+ CD C 0.757964 11
+ OE1 O2 -0.792463 12
+ OE2 O2 -0.792463 13
+ C C 0.731186 14
+ OC1 O2 -0.780593 15
+ OC2 O2 -0.780593 16
[ bonds ]
N H
N CA
[ CASP ]
[ atoms ]
- N N -0.51920 1
- H H 0.30550 2
- CA CT -0.18170 3
- HA H1 0.10460 4
- CB CT -0.06770 5
- HB1 HC -0.02120 6
- HB2 HC -0.02120 7
- CG C 0.88510 8
- OD1 O2 -0.81620 9
- OD2 O2 -0.81620 10
- C C 0.72560 11
- OC1 O2 -0.78870 12
- OC2 O2 -0.78870 13
+ N N -0.649462 1
+ H H 0.426853 2
+ CA CT -0.306286 3
+ HA H1 0.183181 4
+ CB CT -0.078986 5
+ HB1 HC 0.018648 6
+ HB2 HC 0.018648 7
+ CG C 0.844830 8
+ OD1 O2 -0.813714 9
+ OD2 O2 -0.813714 10
+ C C 0.732350 11
+ OC1 O2 -0.781175 12
+ OC2 O2 -0.781175 13
[ bonds ]
N H
N CA
[ CLYS ]
[ atoms ]
- N N -0.34810 1
- H H 0.27640 2
- CA CT -0.29030 3
- HA H1 0.14380 4
- CB CT -0.05380 5
- HB1 HC 0.04820 6
- HB2 HC 0.04820 7
- CG CT 0.02270 8
- HG1 HC 0.01340 9
- HG2 HC 0.01340 10
- CD CT -0.03920 11
- HD1 HC 0.06110 12
- HD2 HC 0.06110 13
- CE CT -0.01760 14
- HE1 HP 0.11210 15
- HE2 HP 0.11210 16
- NZ N3 -0.37410 17
- HZ1 H 0.33740 18
- HZ2 H 0.33740 19
- HZ3 H 0.33740 20
- C C 0.84880 21
- OC1 O2 -0.82520 22
- OC2 O2 -0.82520 23
+ N N -0.629569 1
+ H H 0.357460 2
+ CA CT -0.053541 3
+ HA H1 0.138544 4
+ CB CT -0.046022 5
+ HB1 HC 0.042912 6
+ HB2 HC 0.042912 7
+ CG CT 0.020231 8
+ HG1 HC 0.010971 9
+ HG2 HC 0.010971 10
+ CD CT -0.046165 11
+ HD1 HC 0.061437 12
+ HD2 HC 0.061437 13
+ CE CT -0.032772 14
+ HE1 HP 0.101654 15
+ HE2 HP 0.101654 16
+ NZ N3 -0.168623 17
+ HZ1 H 0.285503 18
+ HZ2 H 0.285503 19
+ HZ3 H 0.285503 20
+ C C 0.541818 21
+ OC1 O2 -0.685909 22
+ OC2 O2 -0.685909 23
[ bonds ]
N H
N CA
[ CPRO ]
[ atoms ]
- N N -0.28020 1
- CD CT 0.04340 2
- HD1 H1 0.03310 3
- HD2 H1 0.03310 4
- CG CT 0.04660 5
- HG1 HC 0.01720 6
- HG2 HC 0.01720 7
- CB CT -0.05430 8
- HB1 HC 0.03810 9
- HB2 HC 0.03810 10
- CA CT -0.13360 11
- HA H1 0.07760 12
- C C 0.66310 13
- OC1 O2 -0.76970 14
- OC2 O2 -0.76970 15
+ N N -0.268742 1
+ CD CT 0.062285 2
+ HD1 H1 0.034717 3
+ HD2 H1 0.034717 4
+ CG CT 0.059879 5
+ HG1 HC 0.007548 6
+ HG2 HC 0.007548 7
+ CB CT 0.065773 8
+ HB1 HC 0.016889 9
+ HB2 HC 0.016889 10
+ CA CT -0.385442 11
+ HA H1 0.177938 12
+ C C 0.643321 13
+ OC1 O2 -0.736661 14
+ OC2 O2 -0.736661 15
[ bonds ]
N CD
N CA
[ CCYS ]
[ atoms ]
- N N -0.38210 1
- H H 0.26810 2
- CA CT -0.16350 3
- HA H1 0.13960 4
- CB CT -0.19960 5
- HB1 H1 0.14370 6
- HB2 H1 0.14370 7
- SG SH -0.31020 8
- HG HS 0.20680 9
- C C 0.74970 10
- OC1 O2 -0.79810 11
- OC2 O2 -0.79810 12
+ N N -0.555037 1
+ H H 0.345483 2
+ CA CT -0.110929 3
+ HA H1 0.147206 4
+ CB CT -0.162428 5
+ HB1 H1 0.131999 6
+ HB2 H1 0.131999 7
+ SG SH -0.290711 8
+ HG HS 0.192419 9
+ C C 0.671942 10
+ OC1 O2 -0.750971 11
+ OC2 O2 -0.750971 12
[ bonds ]
N H
N CA
[ CMET ]
[ atoms ]
- N N -0.38210 1
- H H 0.26810 2
- CA CT -0.25970 3
- HA H1 0.12770 4
- CB CT -0.02360 5
- HB1 HC 0.04800 6
- HB2 HC 0.04800 7
- CG CT 0.04920 8
- HG1 H1 0.03170 9
- HG2 H1 0.03170 10
- SD S -0.26920 11
- CE CT -0.03760 12
- HE1 H1 0.06250 13
- HE2 H1 0.06250 14
- HE3 H1 0.06250 15
- C C 0.80130 16
- OC1 O2 -0.81050 17
- OC2 O2 -0.81050 18
+ N N -0.564246 1
+ H H 0.334412 2
+ CA CT -0.159882 3
+ HA H1 0.142833 4
+ CB CT 0.058364 5
+ HB1 HC 0.052479 6
+ HB2 HC 0.052479 7
+ CG CT -0.230352 8
+ HG1 H1 0.127983 9
+ HG2 H1 0.127983 10
+ SD S -0.218570 11
+ CE CT -0.262571 12
+ HE1 H1 0.123031 13
+ HE2 H1 0.123031 14
+ HE3 H1 0.123031 15
+ C C 0.664918 16
+ OC1 O2 -0.747459 17
+ OC2 O2 -0.747459 18
[ bonds ]
N H
N CA
[ NALA ]
[ atoms ]
- N N3 0.14140 1
- H1 H 0.19970 2
- H2 H 0.19970 3
- H3 H 0.19970 4
- CA CT 0.09620 5
- HA HP 0.08890 6
- CB CT -0.05970 7
- HB1 HC 0.03000 8
- HB2 HC 0.03000 9
- HB3 HC 0.03000 10
- C C 0.61630 11
- O O -0.57220 12
+ N N3 -0.589266 1
+ H1 H 0.446422 2
+ H2 H 0.446422 3
+ H3 H 0.446422 4
+ CA CT 0.113871 5
+ HA HP 0.067150 6
+ CB CT -0.204113 7
+ HB1 HC 0.063056 8
+ HB2 HC 0.063056 9
+ HB3 HC 0.063056 10
+ C C 0.676687 11
+ O O -0.592764 12
[ bonds ]
N H1
N H2
[ NGLY ]
[ atoms ]
- N N3 0.29430 1
- H1 H 0.16420 2
- H2 H 0.16420 3
- H3 H 0.16420 4
- CA CT -0.01000 5
- HA1 HP 0.08950 6
- HA2 HP 0.08950 7
- C C 0.61630 8
- O O -0.57220 9
+ N N3 -0.600766 1
+ H1 H 0.450255 2
+ H2 H 0.450255 3
+ H3 H 0.450255 4
+ CA CT 0.126891 5
+ HA1 HP 0.036849 6
+ HA2 HP 0.036849 7
+ C C 0.648768 8
+ O O -0.599357 9
[ bonds ]
N H1
N H2
[ NSER ]
[ atoms ]
- N N3 0.18490 1
- H1 H 0.18980 2
- H2 H 0.18980 3
- H3 H 0.18980 4
- CA CT 0.05670 5
- HA HP 0.07820 6
- CB CT 0.25960 7
- HB1 H1 0.02730 8
- HB2 H1 0.02730 9
- OG OH -0.67140 10
- HG HO 0.42390 11
- C C 0.61630 12
- O O -0.57220 13
+ N N3 -0.664403 1
+ H1 H 0.471468 2
+ H2 H 0.471468 3
+ H3 H 0.471468 4
+ CA CT 0.140290 5
+ HA HP 0.091150 6
+ CB CT 0.111987 7
+ HB1 H1 0.039285 8
+ HB2 H1 0.039285 9
+ OG OH -0.593805 10
+ HG HO 0.407492 11
+ C C 0.592480 12
+ O O -0.578162 13
[ bonds ]
N H1
N H2
[ NTHR ]
[ atoms ]
- N N3 0.18120 1
- H1 H 0.19340 2
- H2 H 0.19340 3
- H3 H 0.19340 4
- CA CT 0.00340 5
- HA HP 0.10870 6
- CB CT 0.45140 7
- HB H1 -0.03230 8
- CG2 CT -0.25540 9
- HG21 HC 0.06270 10
- HG22 HC 0.06270 11
- HG23 HC 0.06270 12
- OG1 OH -0.67640 13
- HG1 HO 0.40700 14
- C C 0.61630 15
- O O -0.57220 16
+ N N3 -0.570235 1
+ H1 H 0.440078 2
+ H2 H 0.440078 3
+ H3 H 0.440078 4
+ CA CT 0.028754 5
+ HA HP 0.078538 6
+ CB CT 0.270941 7
+ HB H1 -0.014476 8
+ CG2 CT -0.160657 9
+ HG21 HC 0.053833 10
+ HG22 HC 0.053833 11
+ HG23 HC 0.053833 12
+ OG1 OH -0.621934 13
+ HG1 HO 0.409167 14
+ C C 0.709968 15
+ O O -0.611797 16
[ bonds ]
N H1
N H2
[ NLEU ]
[ atoms ]
- N N3 0.10100 1
- H1 H 0.21480 2
- H2 H 0.21480 3
- H3 H 0.21480 4
- CA CT 0.01040 5
- HA HP 0.10530 6
- CB CT -0.02440 7
- HB1 HC 0.02560 8
- HB2 HC 0.02560 9
- CG CT 0.34210 10
- HG HC -0.03800 11
- CD1 CT -0.41060 12
- HD11 HC 0.09800 13
- HD12 HC 0.09800 14
- HD13 HC 0.09800 15
- CD2 CT -0.41040 16
- HD21 HC 0.09800 17
- HD22 HC 0.09800 18
- HD23 HC 0.09800 19
- C C 0.61230 20
- O O -0.57130 21
+ N N3 -0.624705 1
+ H1 H 0.458235 2
+ H2 H 0.458235 3
+ H3 H 0.458235 4
+ CA CT 0.069804 5
+ HA HP 0.092394 6
+ CB CT -0.118019 7
+ HB1 HC 0.037615 8
+ HB2 HC 0.037615 9
+ CG CT 0.177099 10
+ HG HC 0.013272 11
+ CD1 CT -0.157414 12
+ HD11 HC 0.031964 13
+ HD12 HC 0.031964 14
+ HD13 HC 0.031964 15
+ CD2 CT -0.157414 16
+ HD21 HC 0.031964 17
+ HD22 HC 0.031964 18
+ HD23 HC 0.031964 19
+ C C 0.656583 20
+ O O -0.593318 21
[ bonds ]
N H1
N H2
[ NILE ]
[ atoms ]
- N N3 0.03110 1
- H1 H 0.23290 2
- H2 H 0.23290 3
- H3 H 0.23290 4
- CA CT 0.02570 5
- HA HP 0.10310 6
- CB CT 0.18850 7
- HB HC 0.02130 8
- CG2 CT -0.37200 9
- HG21 HC 0.09470 10
- HG22 HC 0.09470 11
- HG23 HC 0.09470 12
- CG1 CT -0.03870 13
- HG11 HC 0.02010 14
- HG12 HC 0.02010 15
- CD CT -0.09080 16
- HD1 HC 0.02260 17
- HD2 HC 0.02260 18
- HD3 HC 0.02260 19
- C C 0.61230 20
- O O -0.57130 21
+ N N3 -0.605757 1
+ H1 H 0.451919 2
+ H2 H 0.451919 3
+ H3 H 0.451919 4
+ CA CT 0.025768 5
+ HA HP 0.062754 6
+ CB CT 0.044198 7
+ HB HC 0.038704 8
+ CG2 CT -0.172672 9
+ HG21 HC 0.038544 10
+ HG22 HC 0.038544 11
+ HG23 HC 0.038544 12
+ CG1 CT 0.058447 13
+ HG11 HC 0.003617 14
+ HG12 HC 0.003617 15
+ CD CT -0.111609 16
+ HD1 HC 0.025639 17
+ HD2 HC 0.025639 18
+ HD3 HC 0.025639 19
+ C C 0.733445 20
+ O O -0.628820 21
[ bonds ]
N H1
N H2
[ NVAL ]
[ atoms ]
- N N3 0.05770 1
- H1 H 0.22720 2
- H2 H 0.22720 3
- H3 H 0.22720 4
- CA CT -0.00540 5
- HA HP 0.10930 6
- CB CT 0.31960 7
- HB HC -0.02210 8
- CG1 CT -0.31290 9
- HG11 HC 0.07350 10
- HG12 HC 0.07350 11
- HG13 HC 0.07350 12
- CG2 CT -0.31290 13
- HG21 HC 0.07350 14
- HG22 HC 0.07350 15
- HG23 HC 0.07350 16
- C C 0.61630 17
- O O -0.57220 18
+ N N3 -0.737450 1
+ H1 H 0.495817 2
+ H2 H 0.495817 3
+ H3 H 0.495817 4
+ CA CT -0.082837 5
+ HA HP 0.017007 6
+ CB CT 0.240887 7
+ HB HC -0.034674 8
+ CG1 CT -0.209130 9
+ HG11 HC 0.043124 10
+ HG12 HC 0.043124 11
+ HG13 HC 0.043124 12
+ CG2 CT -0.209130 13
+ HG21 HC 0.043124 14
+ HG22 HC 0.043124 15
+ HG23 HC 0.043124 16
+ C C 0.890641 17
+ O O -0.621511 18
[ bonds ]
N H1
N H2
[ NASN ]
[ atoms ]
- N N3 0.18010 1
- H1 H 0.19210 2
- H2 H 0.19210 3
- H3 H 0.19210 4
- CA CT 0.03680 5
- HA HP 0.12310 6
- CB CT -0.02830 7
- HB1 HC 0.05150 8
- HB2 HC 0.05150 9
- CG C 0.58330 10
- OD1 O -0.57440 11
- ND2 N -0.86340 12
- HD21 H 0.40970 13
- HD22 H 0.40970 14
- C C 0.61630 15
- O O -0.57220 16
+ N N3 -0.669106 1
+ H1 H 0.473035 2
+ H2 H 0.473035 3
+ H3 H 0.473035 4
+ CA CT 0.256684 5
+ HA HP 0.013306 6
+ CB CT -0.062106 7
+ HB1 HC 0.038289 8
+ HB2 HC 0.038289 9
+ CG C 0.554932 10
+ OD1 O -0.568797 11
+ ND2 N -0.784547 12
+ HD21 H 0.372344 13
+ HD22 H 0.372344 14
+ C C 0.602554 15
+ O O -0.583293 16
[ bonds ]
N H1
N H2
[ NGLN ]
[ atoms ]
- N N3 0.14930 1
- H1 H 0.19960 2
- H2 H 0.19960 3
- H3 H 0.19960 4
- CA CT 0.05360 5
- HA HP 0.10150 6
- CB CT 0.06510 7
- HB1 HC 0.00500 8
- HB2 HC 0.00500 9
- CG CT -0.09030 10
- HG1 HC 0.03310 11
- HG2 HC 0.03310 12
- CD C 0.73540 13
- OE1 O -0.61330 14
- NE2 N -1.00310 15
- HE21 H 0.44290 16
- HE22 H 0.44290 17
- C C 0.61230 18
- O O -0.57130 19
+ N N3 -0.603779 1
+ H1 H 0.451260 2
+ H2 H 0.451260 3
+ H3 H 0.451260 4
+ CA CT 0.201127 5
+ HA HP 0.028930 6
+ CB CT -0.013277 7
+ HB1 HC 0.001827 8
+ HB2 HC 0.001827 9
+ CG CT -0.030707 10
+ HG1 HC 0.024665 11
+ HG2 HC 0.024665 12
+ CD C 0.669568 13
+ OE1 O -0.585802 14
+ NE2 N -0.889652 15
+ HE21 H 0.397306 16
+ HE22 H 0.397306 17
+ C C 0.606634 18
+ O O -0.584415 19
[ bonds ]
N H1
N H2
[ NARG ]
[ atoms ]
- N N3 0.13050 1
- H1 H 0.20830 2
- H2 H 0.20830 3
- H3 H 0.20830 4
- CA CT -0.02230 5
- HA HP 0.12420 6
- CB CT 0.01180 7
- HB1 HC 0.02260 8
- HB2 HC 0.02260 9
- CG CT 0.02360 10
- HG1 HC 0.03090 11
- HG2 HC 0.03090 12
- CD CT 0.09350 13
- HD1 H1 0.05270 14
- HD2 H1 0.05270 15
- NE N2 -0.56500 16
- HE H 0.35920 17
- CZ CA 0.82810 18
- NH1 N2 -0.86930 19
- HH11 H 0.44940 20
- HH12 H 0.44940 21
- NH2 N2 -0.86930 22
- HH21 H 0.44940 23
- HH22 H 0.44940 24
- C C 0.72140 25
- O O -0.60130 26
+ N N3 -0.670515 1
+ H1 H 0.473505 2
+ H2 H 0.473505 3
+ H3 H 0.473505 4
+ CA CT 0.093903 5
+ HA HP 0.024998 6
+ CB CT 0.029171 7
+ HB1 HC 0.028728 8
+ HB2 HC 0.028728 9
+ CG CT -0.016208 10
+ HG1 HC 0.002044 11
+ HG2 HC 0.002044 12
+ CD CT 0.176568 13
+ HD1 H1 0.048477 14
+ HD2 H1 0.048477 15
+ NE N2 -0.450568 16
+ HE H 0.338467 17
+ CZ CA 0.561360 18
+ NH1 N2 -0.706473 19
+ HH11 H 0.405927 20
+ HH12 H 0.405927 21
+ NH2 N2 -0.706473 22
+ HH21 H 0.405927 23
+ HH22 H 0.405927 24
+ C C 0.770284 25
+ O O -0.647234 26
[ bonds ]
N H1
N H2
[ NHID ]
[ atoms ]
- N N3 0.15420 1
- H1 H 0.19630 2
- H2 H 0.19630 3
- H3 H 0.19630 4
- CA CT 0.09640 5
- HA HP 0.09580 6
- CB CT 0.02590 7
- HB1 HC 0.02090 8
- HB2 HC 0.02090 9
- CG CC -0.03990 10
- ND1 NA -0.38190 11
- HD1 H 0.36320 12
- CE1 CR 0.21270 13
- HE1 H5 0.13850 14
- NE2 NB -0.57110 15
- CD2 CV 0.10460 16
- HD2 H4 0.12990 17
- C C 0.61230 18
- O O -0.57130 19
+ N N3 -0.702202 1
+ H1 H 0.484067 2
+ H2 H 0.484067 3
+ H3 H 0.484067 4
+ CA CT 0.270112 5
+ HA HP 0.023946 6
+ CB CT -0.066199 7
+ HB1 HC 0.045493 8
+ HB2 HC 0.045493 9
+ CG CC -0.029295 10
+ ND1 NA -0.217584 11
+ HD1 H 0.293840 12
+ CE1 CR 0.147532 13
+ HE1 H5 0.110099 14
+ NE2 NB -0.551585 15
+ CD2 CV 0.071109 16
+ HD2 H4 0.096199 17
+ C C 0.590651 18
+ O O -0.579809 19
[ bonds ]
N H1
N H2
[ NHIE ]
[ atoms ]
- N N3 0.14720 1
- H1 H 0.20160 2
- H2 H 0.20160 3
- H3 H 0.20160 4
- CA CT 0.02360 5
- HA HP 0.13800 6
- CB CT 0.04890 7
- HB1 HC 0.02230 8
- HB2 HC 0.02230 9
- CG CC 0.17400 10
- ND1 NB -0.55790 11
- CE1 CR 0.18040 12
- HE1 H5 0.13970 13
- NE2 NA -0.27810 14
- HE2 H 0.33240 15
- CD2 CW -0.23490 16
- HD2 H4 0.19630 17
- C C 0.61230 18
- O O -0.57130 19
+ N N3 -0.697797 1
+ H1 H 0.482599 2
+ H2 H 0.482599 3
+ H3 H 0.482599 4
+ CA CT 0.181926 5
+ HA HP 0.060125 6
+ CB CT -0.114822 7
+ HB1 HC 0.057721 8
+ HB2 HC 0.057721 9
+ CG CC 0.209925 10
+ ND1 NB -0.486658 11
+ CE1 CR 0.055422 12
+ HE1 H5 0.126178 13
+ NE2 NA -0.090417 14
+ HE2 H 0.281999 15
+ CD2 CW -0.258671 16
+ HD2 H4 0.154335 17
+ C C 0.601906 18
+ O O -0.586694 19
[ bonds ]
N H1
N H2
[ NHIP ]
[ atoms ]
- N N3 0.25600 1
- H1 H 0.17040 2
- H2 H 0.17040 3
- H3 H 0.17040 4
- CA CT 0.05810 5
- HA HP 0.10470 6
- CB CT 0.04840 7
- HB1 HC 0.05310 8
- HB2 HC 0.05310 9
- CG CC -0.02360 10
- ND1 NA -0.15100 11
- HD1 H 0.38210 12
- CE1 CR -0.00110 13
- HE1 H5 0.26450 14
- NE2 NA -0.17390 15
- HE2 H 0.39210 16
- CD2 CW -0.14330 17
- HD2 H4 0.24950 18
- C C 0.72140 19
- O O -0.60130 20
+ N N3 -0.745211 1
+ H1 H 0.498404 2
+ H2 H 0.498404 3
+ H3 H 0.498404 4
+ CA CT 0.223794 5
+ HA HP 0.029571 6
+ CB CT -0.063494 7
+ HB1 HC 0.089473 8
+ HB2 HC 0.089473 9
+ CG CC -0.005485 10
+ ND1 NA -0.014619 11
+ HD1 H 0.275668 12
+ CE1 CR -0.020417 13
+ HE1 H5 0.220661 14
+ NE2 NA -0.119388 15
+ HE2 H 0.363590 16
+ CD2 CW -0.156771 17
+ HD2 H4 0.221434 18
+ C C 0.737512 19
+ O O -0.621000 20
[ bonds ]
N H1
N H2
[ NTRP ]
[ atoms ]
- N N3 0.19130 1
- H1 H 0.18880 2
- H2 H 0.18880 3
- H3 H 0.18880 4
- CA CT 0.04210 5
- HA HP 0.11620 6
- CB CT 0.05430 7
- HB1 HC 0.02220 8
- HB2 HC 0.02220 9
- CG C* -0.16540 10
- CD1 CW -0.17880 11
- HD1 H4 0.21950 12
- NE1 NA -0.34440 13
- HE1 H 0.34120 14
- CE2 CN 0.15750 15
- CZ2 CA -0.27100 16
- HZ2 HA 0.15890 17
- CH2 CA -0.10800 18
- HH2 HA 0.14110 19
- CZ3 CA -0.20340 20
- HZ3 HA 0.14580 21
- CE3 CA -0.22650 22
- HE3 HA 0.16460 23
- CD2 CB 0.11320 24
- C C 0.61230 25
- O O -0.57130 26
+ N N3 -0.621979 1
+ H1 H 0.457326 2
+ H2 H 0.457326 3
+ H3 H 0.457326 4
+ CA CT 0.117919 5
+ HA HP 0.073247 6
+ CB CT -0.053219 7
+ HB1 HC 0.055273 8
+ HB2 HC 0.055273 9
+ CG C* -0.144090 10
+ CD1 CW -0.172104 11
+ HD1 H4 0.179500 12
+ NE1 NA -0.300089 13
+ HE1 H 0.343546 14
+ CE2 CN 0.145233 15
+ CZ2 CA -0.220933 16
+ HZ2 HA 0.135970 17
+ CH2 CA -0.139029 18
+ HH2 HA 0.123118 19
+ CZ3 CA -0.177371 20
+ HZ3 HA 0.122346 21
+ CE3 CA -0.170285 22
+ HE3 HA 0.135963 23
+ CD2 CB 0.083829 24
+ C C 0.626460 25
+ O O -0.570557 26
[ bonds ]
N H1
N H2
[ NPHE ]
[ atoms ]
- N N3 0.17370 1
- H1 H 0.19210 2
- H2 H 0.19210 3
- H3 H 0.19210 4
- CA CT 0.07330 5
- HA HP 0.10410 6
- CB CT 0.03300 7
- HB1 HC 0.01040 8
- HB2 HC 0.01040 9
- CG CA 0.00310 10
- CD1 CA -0.13920 11
- HD1 HA 0.13740 12
- CE1 CA -0.16020 13
- HE1 HA 0.14330 14
- CZ CA -0.12080 15
- HZ HA 0.13290 16
- CE2 CA -0.16030 17
- HE2 HA 0.14330 18
- CD2 CA -0.13910 19
- HD2 HA 0.13740 20
- C C 0.61230 21
- O O -0.57130 22
+ N N3 -0.629494 1
+ H1 H 0.459831 2
+ H2 H 0.459831 3
+ H3 H 0.459831 4
+ CA CT 0.175018 5
+ HA HP 0.051530 6
+ CB CT -0.056597 7
+ HB1 HC 0.044331 8
+ HB2 HC 0.044331 9
+ CG CA 0.000827 10
+ CD1 CA -0.101529 11
+ HD1 HA 0.108610 12
+ CE1 CA -0.156341 13
+ HE1 HA 0.128346 14
+ CZ CA -0.104791 15
+ HZ HA 0.119084 16
+ CE2 CA -0.156341 17
+ HE2 HA 0.128346 18
+ CD2 CA -0.101529 19
+ HD2 HA 0.108610 20
+ C C 0.596118 21
+ O O -0.578021 22
[ bonds ]
N H1
N H2
[ NTYR ]
[ atoms ]
- N N3 0.19400 1
- H1 H 0.18730 2
- H2 H 0.18730 3
- H3 H 0.18730 4
- CA CT 0.05700 5
- HA HP 0.09830 6
- CB CT 0.06590 7
- HB1 HC 0.01020 8
- HB2 HC 0.01020 9
- CG CA -0.02050 10
- CD1 CA -0.20020 11
- HD1 HA 0.17200 12
- CE1 CA -0.22390 13
- HE1 HA 0.16500 14
- CZ C 0.31390 15
- OH OH -0.55780 16
- HH HO 0.40010 17
- CE2 CA -0.22390 18
- HE2 HA 0.16500 19
- CD2 CA -0.20020 20
- HD2 HA 0.17200 21
- C C 0.61230 22
- O O -0.57130 23
+ N N3 -0.592849 1
+ H1 H 0.447616 2
+ H2 H 0.447616 3
+ H3 H 0.447616 4
+ CA CT 0.090652 5
+ HA HP 0.113265 6
+ CB CT -0.050705 7
+ HB1 HC 0.006441 8
+ HB2 HC 0.006441 9
+ CG CA 0.130909 10
+ CD1 CA -0.198282 11
+ HD1 HA 0.148246 12
+ CE1 CA -0.213863 13
+ HE1 HA 0.148090 14
+ CZ C 0.242629 15
+ OH OH -0.475387 16
+ HH HO 0.370782 17
+ CE2 CA -0.213863 18
+ HE2 HA 0.148090 19
+ CD2 CA -0.198282 20
+ HD2 HA 0.148246 21
+ C C 0.620893 22
+ O O -0.574301 23
[ bonds ]
N H1
N H2
[ NGLU ]
[ atoms ]
- N N3 0.00170 1
- H1 H 0.23910 2
- H2 H 0.23910 3
- H3 H 0.23910 4
- CA CT 0.05880 5
- HA HP 0.12020 6
- CB CT 0.09090 7
- HB1 HC -0.02320 8
- HB2 HC -0.02320 9
- CG CT -0.02360 10
- HG1 HC -0.03150 11
- HG2 HC -0.03150 12
- CD C 0.80870 13
- OE1 O2 -0.81890 14
- OE2 O2 -0.81890 15
- C C 0.56210 16
- O O -0.58890 17
+ N N3 -0.465328 1
+ H1 H 0.405109 2
+ H2 H 0.405109 3
+ H3 H 0.405109 4
+ CA CT 0.127199 5
+ HA HP 0.023038 6
+ CB CT 0.088282 7
+ HB1 HC -0.034219 8
+ HB2 HC -0.034219 9
+ CG CT -0.009673 10
+ HG1 HC -0.021524 11
+ HG2 HC -0.021524 12
+ CD C 0.740015 13
+ OE1 O2 -0.780545 14
+ OE2 O2 -0.780545 15
+ C C 0.552551 16
+ O O -0.598835 17
[ bonds ]
N H1
N H2
[ NASP ]
[ atoms ]
- N N3 0.07820 1
- H1 H 0.22000 2
- H2 H 0.22000 3
- H3 H 0.22000 4
- CA CT 0.02920 5
- HA HP 0.11410 6
- CB CT -0.02350 7
- HB1 HC -0.01690 8
- HB2 HC -0.01690 9
- CG C 0.81940 10
- OD1 O2 -0.80840 11
- OD2 O2 -0.80840 12
- C C 0.56210 13
- O O -0.58890 14
+ N N3 -0.588807 1
+ H1 H 0.446269 2
+ H2 H 0.446269 3
+ H3 H 0.446269 4
+ CA CT 0.015024 5
+ HA HP 0.090798 6
+ CB CT -0.071792 7
+ HB1 HC 0.002802 8
+ HB2 HC 0.002802 9
+ CG C 0.770432 10
+ OD1 O2 -0.787966 11
+ OD2 O2 -0.787966 12
+ C C 0.602072 13
+ O O -0.586206 14
[ bonds ]
N H1
N H2
[ NLYS ]
[ atoms ]
- N N3 0.09660 1
- H1 H 0.21650 2
- H2 H 0.21650 3
- H3 H 0.21650 4
- CA CT -0.00150 5
- HA HP 0.11800 6
- CB CT 0.02120 7
- HB1 HC 0.02830 8
- HB2 HC 0.02830 9
- CG CT -0.00480 10
- HG1 HC 0.01210 11
- HG2 HC 0.01210 12
- CD CT -0.06080 13
- HD1 HC 0.06330 14
- HD2 HC 0.06330 15
- CE CT -0.01810 16
- HE1 HP 0.11710 17
- HE2 HP 0.11710 18
- NZ N3 -0.37640 19
- HZ1 H 0.33820 20
- HZ2 H 0.33820 21
- HZ3 H 0.33820 22
- C C 0.72140 23
- O O -0.60130 24
+ N N3 -0.743778 1
+ H1 H 0.497926 2
+ H2 H 0.497926 3
+ H3 H 0.497926 4
+ CA CT 0.163115 5
+ HA HP 0.070671 6
+ CB CT -0.044702 7
+ HB1 HC 0.023815 8
+ HB2 HC 0.023815 9
+ CG CT 0.007065 10
+ HG1 HC 0.017881 11
+ HG2 HC 0.017881 12
+ CD CT -0.061357 13
+ HD1 HC 0.065779 14
+ HD2 HC 0.065779 15
+ CE CT -0.029056 16
+ HE1 HP 0.102772 17
+ HE2 HP 0.102772 18
+ NZ N3 -0.181839 19
+ HZ1 H 0.289529 20
+ HZ2 H 0.289529 21
+ HZ3 H 0.289529 22
+ C C 0.633667 23
+ O O -0.596645 24
[ bonds ]
N H1
N H2
[ NPRO ]
[ atoms ]
- N N3 -0.20200 1
- H1 H 0.31200 2
- H2 H 0.31200 3
- CD CT -0.01200 4
- HD1 HP 0.10000 5
- HD2 HP 0.10000 6
- CG CT -0.12100 7
- HG1 HC 0.10000 8
- HG2 HC 0.10000 9
- CB CT -0.11500 10
- HB1 HC 0.10000 11
- HB2 HC 0.10000 12
- CA CT 0.10000 13
- HA HP 0.10000 14
- C C 0.52600 15
- O O -0.50000 16
+ N N3 -0.421739 1
+ H1 H 0.471857 2
+ H2 H 0.471857 3
+ CD CT 0.048486 4
+ HD1 HP 0.039901 5
+ HD2 HP 0.039901 6
+ CG CT 0.106081 7
+ HG1 HC -0.000632 8
+ HG2 HC -0.000632 9
+ CB CT -0.123305 10
+ HB1 HC 0.028355 11
+ HB2 HC 0.028355 12
+ CA CT 0.251986 13
+ HA HP -0.021715 14
+ C C 0.680470 15
+ O O -0.599226 16
[ bonds ]
N H1
N H2
[ NCYS ]
[ atoms ]
- N N3 0.13250 1
- H1 H 0.20230 2
- H2 H 0.20230 3
- H3 H 0.20230 4
- CA CT 0.09270 5
- HA HP 0.14110 6
- CB CT -0.11950 7
- HB1 H1 0.11880 8
- HB2 H1 0.11880 9
- SG SH -0.32980 10
- HG HS 0.19750 11
- C C 0.61230 12
- O O -0.57130 13
+ N N3 -0.610355 1
+ H1 H 0.453452 2
+ H2 H 0.453452 3
+ H3 H 0.453452 4
+ CA CT 0.072150 5
+ HA HP 0.083203 6
+ CB CT -0.155113 7
+ HB1 H1 0.113742 8
+ HB2 H1 0.113742 9
+ SG SH -0.293380 10
+ HG HS 0.190705 11
+ C C 0.747857 12
+ O O -0.622908 13
[ bonds ]
N H1
N H2
[ NMET ]
[ atoms ]
- N N3 0.15920 1
- H1 H 0.19840 2
- H2 H 0.19840 3
- H3 H 0.19840 4
- CA CT 0.02210 5
- HA HP 0.11160 6
- CB CT 0.08650 7
- HB1 HC 0.01250 8
- HB2 HC 0.01250 9
- CG CT 0.03340 10
- HG1 H1 0.02920 11
- HG2 H1 0.02920 12
- SD S -0.27740 13
- CE CT -0.03410 14
- HE1 H1 0.05970 15
- HE2 H1 0.05970 16
- HE3 H1 0.05970 17
- C C 0.61230 18
- O O -0.57130 19
+ N N3 -0.597213 1
+ H1 H 0.449071 2
+ H2 H 0.449071 3
+ H3 H 0.449071 4
+ CA CT 0.060906 5
+ HA HP 0.075421 6
+ CB CT 0.051523 7
+ HB1 HC 0.038926 8
+ HB2 HC 0.038926 9
+ CG CT -0.254386 10
+ HG1 H1 0.129517 11
+ HG2 H1 0.129517 12
+ SD S -0.206852 13
+ CE CT -0.284358 14
+ HE1 H1 0.128754 15
+ HE2 H1 0.128754 16
+ HE3 H1 0.128754 17
+ C C 0.683639 18
+ O O -0.599042 19
[ bonds ]
N H1
N H2
-402
+414
If You Want Something Done You Have to Do It Yourself_(Highlander II)
I Live the Life They Wish They Did_(Tricky)
Jesus Built My Hotrod_(Ministry)
The soul? There's nothing but chemistry here_(Breaking Bad)
You got one part of that wrong. This is not meth._(Breaking Bad)
It's easy to remember: a half a kT is equal to five fourths of a kJ/mol._(Anders Gabrielsson)
+Ubiquitin's just a rock_(Berk Hess)
+... an excellent man, almost worthy of such a wife ..._(Jane Eyre in Jane Eyre by Charlotte Bronte)
+Humbug! Most things free-born will submit to anything for a salary_(Mr. Rochester in Jane Eyre by Charlotte Bronte)
+Like other defaulters, I like to lay half the blame on ill-fortune and adverse circumstances_(Mr. Rochester in Jane Eyre by Charlotte Bronte)
+Either you will be dashed to atoms on crag points, or lifted up and borne by some master-wave into a calmer current_(Charlotte Bronte)
+I ought to warn you, I have no faith_(Jane Eyre in Jane Eyre by Charlotte Bronte)
+... yet the [economic] profession continued to churn out purely theoretical results without even knowing what facts needed to be explained._(Thomas Piketty)
+Scientists think they are born with logic; God forbid they should study this discipline with a history of more than two and a half millennia._(Roald Hoffmann)
+In the processing of models we must be especially cautious of the human weakness to think that models can be verified or validated. Especially one's own._(Roald Hoffmann)
+... and that dream of dreams, a computational model that predicts everything accurately._(Roald Hoffmann)
+You see it through a charmed medium: you can not discern that the gilding is slime and the silk draperies cobwebs; that the marble is sordid slate, and the polished woods mere refuse chips and scale bark._(Mr. Rochester in Jane Eyre by Charlotte Bronte)
+I know poetry is not dead, nor genius lost; nor has Mammon gained power over either, to bind or slay; they will both assert their existence, their presence, their liberty and strength again one day._(Jane Eyre in Jane Eyre by Charlotte Bronte)
}
static void einstein_visco(const char *fn, const char *fni, int nsets,
- int nframes, real **sum,
- real V, real T, int nsteps, double time[],
+ int nint, real **eneint,
+ real V, real T, double dt,
const output_env_t oenv)
{
FILE *fp0, *fp1;
double av[4], avold[4];
- double fac, dt, di;
+ double fac, di;
int i, j, m, nf4;
- if (nframes < 1)
- {
- return;
- }
-
- dt = (time[1]-time[0]);
- nf4 = nframes/4+1;
+ nf4 = nint/4 + 1;
for (i = 0; i <= nsets; i++)
{
"Time (ps)", "(kg m\\S-1\\N s\\S-1\\N ps)", oenv);
fp1 = xvgropen(fn, "Shear viscosity using Einstein relation",
"Time (ps)", "(kg m\\S-1\\N s\\S-1\\N)", oenv);
- for (i = 1; i < nf4; i++)
+ for (i = 0; i < nf4; i++)
{
- fac = dt*nframes/nsteps;
for (m = 0; m <= nsets; m++)
{
av[m] = 0;
}
- for (j = 0; j < nframes-i; j++)
+ for (j = 0; j < nint - i; j++)
{
for (m = 0; m < nsets; m++)
{
- di = sqr(fac*(sum[m][j+i]-sum[m][j]));
+ di = sqr(eneint[m][j+i] - eneint[m][j]);
av[m] += di;
av[nsets] += di/nsets;
}
}
/* Convert to SI for the viscosity */
- fac = (V*NANO*NANO*NANO*PICO*1e10)/(2*BOLTZMANN*T)/(nframes-i);
- fprintf(fp0, "%10g", time[i]-time[0]);
+ fac = (V*NANO*NANO*NANO*PICO*1e10)/(2*BOLTZMANN*T)/(nint - i);
+ fprintf(fp0, "%10g", i*dt);
for (m = 0; (m <= nsets); m++)
{
av[m] = fac*av[m];
fprintf(fp0, " %10g", av[m]);
}
fprintf(fp0, "\n");
- fprintf(fp1, "%10g", 0.5*(time[i]+time[i-1])-time[0]);
+ fprintf(fp1, "%10g", (i + 0.5)*dt);
for (m = 0; (m <= nsets); m++)
{
fprintf(fp1, " %10g", (av[m]-avold[m])/dt);
gmx_bool bVisco, const char *visfn, int nmol,
gmx_int64_t start_step, double start_t,
gmx_int64_t step, double t,
- double time[], real reftemp,
+ real reftemp,
enerdata_t *edat,
int nset, int set[], gmx_bool *bIsEner,
char **leg, gmx_enxnm_t *enm,
const char* leg[] = { "Shear", "Bulk" };
real factor;
real **eneset;
- real **enesum;
+ real **eneint;
/* Assume pressure tensor is in Pxx Pxy Pxz Pyx Pyy Pyz Pzx Pzy Pzz */
{
snew(eneset[i], edat->nframes);
}
- snew(enesum, 3);
- for (i = 0; i < 3; i++)
- {
- snew(enesum[i], edat->nframes);
- }
for (i = 0; (i < edat->nframes); i++)
{
eneset[0][i] = 0.5*(edat->s[1].ener[i]+edat->s[3].ener[i]);
eneset[j][i] = edat->s[j].ener[i];
}
eneset[11][i] -= Pres;
- enesum[0][i] = 0.5*(edat->s[1].es[i].sum+edat->s[3].es[i].sum);
- enesum[1][i] = 0.5*(edat->s[2].es[i].sum+edat->s[6].es[i].sum);
- enesum[2][i] = 0.5*(edat->s[5].es[i].sum+edat->s[7].es[i].sum);
+ }
+
+ /* Determine integrals of the off-diagonal pressure elements */
+ snew(eneint, 3);
+ for (i = 0; i < 3; i++)
+ {
+ snew(eneint[i], edat->nframes + 1);
+ }
+ eneint[0][0] = 0;
+ eneint[1][0] = 0;
+ eneint[2][0] = 0;
+ for (i = 0; i < edat->nframes; i++)
+ {
+ eneint[0][i+1] = eneint[0][i] + 0.5*(edat->s[1].es[i].sum + edat->s[3].es[i].sum)*Dt/edat->points[i];
+ eneint[1][i+1] = eneint[1][i] + 0.5*(edat->s[2].es[i].sum + edat->s[6].es[i].sum)*Dt/edat->points[i];
+ eneint[2][i+1] = eneint[2][i] + 0.5*(edat->s[5].es[i].sum + edat->s[7].es[i].sum)*Dt/edat->points[i];
}
einstein_visco("evisco.xvg", "eviscoi.xvg",
- 3, edat->nframes, enesum, Vaver, Temp, nsteps, time, oenv);
+ 3, edat->nframes+1, eneint, Vaver, Temp, Dt, oenv);
+
+ for (i = 0; i < 3; i++)
+ {
+ sfree(eneint[i]);
+ }
+ sfree(eneint);
/*do_autocorr(corrfn,buf,nenergy,3,eneset,Dt,eacNormal,TRUE);*/
/* Do it for shear viscosity */
fprintf(fp, "%10g %10g %10g\n", (i*Dt), integral, intBulk);
}
gmx_ffclose(fp);
+
+ for (i = 0; i < 12; i++)
+ {
+ sfree(eneset[i]);
+ }
+ sfree(eneset);
}
else if (bCorr)
{
bVisco, opt2fn("-vis", NFILE, fnm),
nmol,
start_step, start_t, frame[cur].step, frame[cur].t,
- time, reftemp, &edat,
+ reftemp, &edat,
nset, set, bIsEner, leg, enm, Vaver, ezero, nbmin, nbmax,
oenv);
if (bFluctProps)
gmx_bool bTwinRange;
int nlr;
rvec *f_twin;
+ /* Constraint virial correction for multiple time stepping */
+ tensor vir_twin_constr;
/* Forces that should not enter into the virial summation:
* PPPM/PME/Ewald/posres
rvec *f, /* forces on home particles */
gmx_bool bDoLR,
rvec *f_lr,
+ tensor *vir_lr_constr,
t_fcdata *fcd,
gmx_ekindata_t *ekind,
matrix M,
}
}
-static void combine_forces(int nstcalclr,
- gmx_constr_t constr,
- t_inputrec *ir, t_mdatoms *md, t_idef *idef,
- t_commrec *cr,
- gmx_int64_t step,
- t_state *state, gmx_bool bMolPBC,
- int start, int nrend,
- rvec f[], rvec f_lr[],
- t_nrnb *nrnb)
-{
- int i, d, nm1;
-
- /* f contains the short-range forces + the long range forces
- * which are stored separately in f_lr.
- */
-
- if (constr != NULL && !(ir->eConstrAlg == econtSHAKE && ir->epc == epcNO))
- {
- /* We need to constrain the LR forces separately,
- * because due to the different pre-factor for the SR and LR
- * forces in the update algorithm, we can not determine
- * the constraint force for the coordinate constraining.
- * Constrain only the additional LR part of the force.
- */
- /* MRS -- need to make sure this works with trotter integration -- the constraint calls may not be right.*/
- constrain(NULL, FALSE, FALSE, constr, idef, ir, NULL, cr, step, 0, md,
- state->x, f_lr, f_lr, bMolPBC, state->box, state->lambda[efptBONDED], NULL,
- NULL, NULL, nrnb, econqForce, ir->epc == epcMTTK, state->veta, state->veta);
- }
-
- /* Add nstcalclr-1 times the LR force to the sum of both forces
- * and store the result in forces_lr.
- */
- nm1 = nstcalclr - 1;
- for (i = start; i < nrend; i++)
- {
- for (d = 0; d < DIM; d++)
- {
- f_lr[i][d] = f[i][d] + nm1*f_lr[i][d];
- }
- }
-}
-
void update_tcouple(gmx_int64_t step,
t_inputrec *inputrec,
t_state *state,
return upd->xp;
}
+static void combine_forces(gmx_update_t upd,
+ int nstcalclr,
+ gmx_constr_t constr,
+ t_inputrec *ir, t_mdatoms *md, t_idef *idef,
+ t_commrec *cr,
+ gmx_int64_t step,
+ t_state *state, gmx_bool bMolPBC,
+ int start, int nrend,
+ rvec f[], rvec f_lr[],
+ tensor *vir_lr_constr,
+ t_nrnb *nrnb)
+{
+ int i, d;
+
+ /* f contains the short-range forces + the long range forces
+ * which are stored separately in f_lr.
+ */
+
+ if (constr != NULL && vir_lr_constr != NULL &&
+ !(ir->eConstrAlg == econtSHAKE && ir->epc == epcNO))
+ {
+ /* We need to constrain the LR forces separately,
+ * because due to the different pre-factor for the SR and LR
+ * forces in the update algorithm, we have to correct
+ * the constraint virial for the nstcalclr-1 extra f_lr.
+ * Constrain only the additional LR part of the force.
+ */
+ /* MRS -- need to make sure this works with trotter integration -- the constraint calls may not be right.*/
+ rvec *xp;
+ real fac;
+ int gf = 0;
+
+ xp = get_xprime(state, upd);
+
+ fac = (nstcalclr - 1)*ir->delta_t*ir->delta_t;
+
+ for (i = 0; i < md->homenr; i++)
+ {
+ if (md->cFREEZE != NULL)
+ {
+ gf = md->cFREEZE[i];
+ }
+ for (d = 0; d < DIM; d++)
+ {
+ if ((md->ptype[i] != eptVSite) &&
+ (md->ptype[i] != eptShell) &&
+ !ir->opts.nFreeze[gf][d])
+ {
+ xp[i][d] = state->x[i][d] + fac*f_lr[i][d]*md->invmass[i];
+ }
+ }
+ }
+ constrain(NULL, FALSE, FALSE, constr, idef, ir, NULL, cr, step, 0, md,
+ state->x, xp, xp, bMolPBC, state->box, state->lambda[efptBONDED], NULL,
+ NULL, vir_lr_constr, nrnb, econqCoord, ir->epc == epcMTTK, state->veta, state->veta);
+ }
+
+ /* Add nstcalclr-1 times the LR force to the sum of both forces
+ * and store the result in forces_lr.
+ */
+ for (i = start; i < nrend; i++)
+ {
+ for (d = 0; d < DIM; d++)
+ {
+ f_lr[i][d] = f[i][d] + (nstcalclr - 1)*f_lr[i][d];
+ }
+ }
+}
+
void update_constraints(FILE *fplog,
gmx_int64_t step,
real *dvdlambda, /* the contribution to be added to the bonded interactions */
rvec *f, /* forces on home particles */
gmx_bool bDoLR,
rvec *f_lr,
+ tensor *vir_lr_constr,
t_fcdata *fcd,
gmx_ekindata_t *ekind,
matrix M,
* to produce twin time stepping.
*/
/* is this correct in the new construction? MRS */
- combine_forces(inputrec->nstcalclr, constr, inputrec, md, idef, cr,
+ combine_forces(upd,
+ inputrec->nstcalclr, constr, inputrec, md, idef, cr,
step, state, bMolPBC,
- start, nrend, f, f_lr, nrnb);
+ start, nrend, f, f_lr, vir_lr_constr, nrnb);
force = f_lr;
}
else
bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC,
- f, bUpdateDoLR, fr->f_twin, fcd,
+ f, bUpdateDoLR, fr->f_twin, bCalcVir ? &fr->vir_twin_constr : NULL, fcd,
ekind, M, upd, bInitStep, etrtVELOCITY1,
cr, nrnb, constr, &top->idef);
cr, nrnb, wcycle, upd, constr,
TRUE, bCalcVir, vetanew);
+ if (bCalcVir && bUpdateDoLR && ir->nstcalclr > 1)
+ {
+ /* Correct the virial for multiple time stepping */
+ m_sub(shake_vir, fr->vir_twin_constr, shake_vir);
+ }
+
if (!bOK)
{
gmx_fatal(FARGS, "Constraint error: Shake, Lincs or Settle could not solve the constrains");
/* velocity half-step update */
update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
- bUpdateDoLR, fr->f_twin, fcd,
+ bUpdateDoLR, fr->f_twin, bCalcVir ? &fr->vir_twin_constr : NULL, fcd,
ekind, M, upd, FALSE, etrtVELOCITY2,
cr, nrnb, constr, &top->idef);
}
bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
- bUpdateDoLR, fr->f_twin, fcd,
+ bUpdateDoLR, fr->f_twin, bCalcVir ? &fr->vir_twin_constr : NULL, fcd,
ekind, M, upd, bInitStep, etrtPOSITION, cr, nrnb, constr, &top->idef);
wallcycle_stop(wcycle, ewcUPDATE);
cr, nrnb, wcycle, upd, constr,
FALSE, bCalcVir, state->veta);
+ if (bCalcVir && bUpdateDoLR && ir->nstcalclr > 1)
+ {
+ /* Correct the virial for multiple time stepping */
+ m_sub(shake_vir, fr->vir_twin_constr, shake_vir);
+ }
+
if (ir->eI == eiVVAK)
{
/* erase F_EKIN and F_TEMP here? */
bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC, f,
- bUpdateDoLR, fr->f_twin, fcd,
+ bUpdateDoLR, fr->f_twin, bCalcVir ? &fr->vir_twin_constr : NULL, fcd,
ekind, M, upd, bInitStep, etrtPOSITION, cr, nrnb, constr, &top->idef);
wallcycle_stop(wcycle, ewcUPDATE);
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff