/usr/share/gromacs/top/charmm27.ff/aminoacids.c.tdb is in gromacs-data 2018.1-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 | [ None ]
[ COO- ]
[ replace ]
C C CC 12.011 0.34
O OT1 OC 15.9994 -0.67
OXT OT2 OC 15.9994 -0.67
[ add ]
2 8 OT C CA N
OC 15.9994 -0.67 -1
[ impropers ]
C CA OT2 OT1
[ COOH ]
[ replace ]
C C CD 12.011 0.72
O OT1 OB 15.9994 -0.55
OXT OT2 OH 15.9994 -0.61
[ add ]
2 8 OT C CA N
OB 15.9994 -0.55 -1
1 2 HT2 OT2 C CA
H 1.008 0.44 -1
[ replace ]
OT2 OT2 OH1 15.9994 -0.61
[ impropers ]
C CA OT2 OT1
[ CT2 ]
[ replace ]
C CC 12.011 0.55
O O 15.9994 -0.55
[ add ]
1 2 NT C CA N
NH2 14.0027 -0.62 -1
2 3 HT NT C CA
H 1.008 0.00 -1
[ replace ]
HT1 H 1.008 0.30 ; this one is trans to O
HT2 H 1.008 0.32 ; this one is cis to O
[ impropers ]
C NT CA O
C CA NT O
NT C HT1 HT2
NT C HT2 HT1
[ CT3 ]
; N-Methylamide C-terminus
;
; |
; C=O
; |
; NT-HNT
; |
; HT1-CAT-HT3
; |
; HT2
;
[ delete ]
OXT
[ add ]
1 8 NT C CA N
NH1 14.0027 -0.47 -1
1 2 HNT NT C O
H 1.008 0.31 -1
1 8 CAT NT C O
CT3 12.011 -0.11 -1
3 4 HT CAT NT C
HA 1.008 0.09 -1
[ bonds ]
NT CAT ; otherwise CAT does not get bonded to other atoms...
[ impropers ]
NT C CAT HNT
C CA NT O
[ cmap ]
-C N CA C NT
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