[gmx-users] Regarding ffG43a1p force field
Ramachandran G
gtrama at gmail.com
Thu Jun 23 09:13:25 CEST 2011
For the GFP chromophore i name residue as CRIH.
1. aminoacids.rtp
CB2 CB 0.019103 1
CA2 CC -0.026635 2
N2 NB -0.436463 3
C1 CC 0.302706 4
N3 NB -0.541478 5
C2 C 0.563844 6
OC2 O -0.394118 7
CG2 CA -0.079330 8
CZ CA 0.240178 9
CD1 CA -0.072596 10
HD1 HA 0.129374 11
CD2 CA -0.070677 12
HD2 HA 0.091532 13
CE1 CA -0.129374 14
HE1 HA 0.091792 15
CE2 CA -0.087778 16
HE2 HA 0.112301 17
OH OH -0.454413 18
H H 0.37107 19
HH HO 0.258435 20
N N -0.61682 21
CA1 CT -0.116631 22
CB1 CT -0.03127 23
OG1 OH -0.74662 24
HG1 HO 0.45887 25
HB2 H2 0.116716 26
CA3 CT -0.250251 27
C C 0.35254 28
O O -0.48366 29
[ bonds ]
C1 CA1
N3 CA3
N3 C1
N3 C2
C2 OC2
C1 N2
C2 CA2
N2 CA2
CA2 CB2
CB2 CG2
CG2 CD1
CG2 CD2
CD1 CE1
CD2 CE2
CE1 CZ
CE2 CZ
CZ OH
CB1 OG1
OH HH
CB2 HB2
CD1 HD1
CD2 HD2
CE1 HE1
CE2 HE2
CA1 N
CA1 CB1
CA3 C
C O
OG1 CB1
OG1 HG1
N H
-C N
+N C
[ angles ]
; ai aj ak th0 cth ub0 cub
N2 C1 N3 114.0 1087.87
C1 N2 CA2 106.0 1087.87
C1 N3 C2 107.9 1087.87
N2 CA2 C2 108.3 1087.87
N2 CA2 CB2 129.5 376.56
C2 N3 CA3 123.4 267.776
N3 C2 OC2 126.0 351.456
N3 C2 CA2 103.0 1087.87
OC2 C2 CA2 132.0 317.984
C2 CA2 CB2 122.0 376.56
CA2 CB2 CG2 130.0 1087.87
CB2 CG2 CD1 121.0 383.2544
CB2 CG2 CD2 121.0 383.2544
CG2 CD1 CE1 120.0 334.72
CG2 CD2 CE2 120.0 334.72
CD1 CG2 CD2 120.0 334.72
CD1 CE1 CZ 120.0 334.72
CD2 CE2 CZ 120.0 334.72
CE1 CZ CE2 120.0 334.72
OH CZ CE1 120.0 378.2336
OH CZ CE2 120.0 378.2336
HH OH CZ 108.0 543.92
HG1 OG1 CB1 108.0 543.92
N2 C1 CA1 125.0 334.72
N3 C1 CA1 121.4 292.88
C1 N3 CA3 129.0 301.248
HB2 CB2 CA2 114.0 351.456
HB2 CB2 CG2 116.0 351.456
HD1 CD1 CG2 120.0 251.04
HD1 CD1 CE1 120.0 251.04
HD2 CD2 CG2 120.0 251.04
HD2 CD2 CE2 120.0 251.04
HE1 CE1 CZ 120.0 251.04
HE1 CE1 CD1 120.0 251.04
HE2 CE2 CZ 120.0 251.04
HE2 CE2 CD2 120.0 251.04
CA1 N H 118.4 317.984
CA1 CB1 OG1 109.5 669.44
N CA1 CB1 109.7 669.44
CB1 CA1 C1 111.1 527.184
CA3 C O 120.4 669.44
N CA1 C1 110.1 527.184
C CA3 N3 110.3 669.44
CA3 C N 116.6 585.76
C2 CA2 CB2 CG2 ;
N2 CA2 CB2 CG2
CA2 CB2 CG2 CD1 ;
CA2 CB2 CG2 CD2 ;
N2 CA2 CB2 HB2
C2 CA2 CB2 HB2
HB2 CB2 CG2 CD1 ;
HB2 CB2 CG2 CD2 ;
CB2 CG2 CD1 CE1 ;
CB2 CG2 CD2 CE2 ;
CD1 CE1 CZ CE2
CD1 CE1 CZ OH
CE1 CZ OH HH
CE2 CZ OH HH
CG2 CD1 CE1 CZ
HD1 CD1 CG2 CD2
HD1 CD1 CE1 CZ
HD2 CD2 CG2 CD1
HD2 CD2 CE2 CZ
HE1 CE1 CD1 CG2
HE1 CE1 CZ CE2
HE2 CE2 CD2 CG2
HE2 CE2 CZ CE1
CA1 C1 N2 CA2 ;
CA1 C1 N3 C2 ;
CA3 N3 C2 CA2
CA3 N3 C1 N2 ;
CG2 CB2 CA2 N2 ; repeated
CG2 CB2 CA2 C2 ; repeated
CB2 CA2 N2 C1
CB2 CA2 C2 N3
CA2 N2 C1 N3
CA2 C2 N3 C1
OG1 CB1 CA1 C1 ;
OG1 CB1 CA1 N ;
CA1 CB1 OG1 HG1 ;
N3 CA3 C O ;
OC2 C2 CA2 CB2 ;
OC2 C2 N3 CA3 ;
OC2 C2 CA2 N2 ;
OC2 C2 N3 C1 ;
N3 CA3 C +N ; added to link the neighbouring valine
CA3 C +N +H ;
CA3 C +N +CA ;
CB1 CA1 N -C ; added to link the neighbouring PHE
C1 CA1 N -C ;
CA1 N -C -O ;
H N -C -O ; n
[ impropers ]
C1 CA1 N2 N3
CA2 N2 CB2 C2
C2 CA2 OC2 N3
CG2 CB2 CD1 CD2
CZ CE1 CE2 OH
N3 C1 C2 CA3
CB2 CA2 CG2 HB2
CD1 CG2 HD1 CE1
CD2 CG2 HD2 CE2
CE1 CD1 HE1 CZ
CE2 CD2 HE2 CZ
CA1 N C1 CB1
C CA3 N O ;
N CA1 C H ;
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