/usr/share/gromacs/top/amber99sb.ff/ffnonbonded.itp is in gromacs-data 4.5.5-2.
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 | [ atomtypes ]
; name at.num mass charge ptype sigma epsilon
Br 35 79.90 0.0000 A 0.00000e+00 0.00000e+00
C 6 12.01 0.0000 A 3.39967e-01 3.59824e-01
CA 6 12.01 0.0000 A 3.39967e-01 3.59824e-01
CB 6 12.01 0.0000 A 3.39967e-01 3.59824e-01
CC 6 12.01 0.0000 A 3.39967e-01 3.59824e-01
CK 6 12.01 0.0000 A 3.39967e-01 3.59824e-01
CM 6 12.01 0.0000 A 3.39967e-01 3.59824e-01
CN 6 12.01 0.0000 A 3.39967e-01 3.59824e-01
CQ 6 12.01 0.0000 A 3.39967e-01 3.59824e-01
CR 6 12.01 0.0000 A 3.39967e-01 3.59824e-01
CT 6 12.01 0.0000 A 3.39967e-01 4.57730e-01
CV 6 12.01 0.0000 A 3.39967e-01 3.59824e-01
CW 6 12.01 0.0000 A 3.39967e-01 3.59824e-01
C* 6 12.01 0.0000 A 3.39967e-01 3.59824e-01
C0 20 40.08 0.0000 A 3.05240e-01 1.92376e+00
F 9 19.00 0.0000 A 3.11815e-01 2.55224e-01
H 1 1.008 0.0000 A 1.06908e-01 6.56888e-02
HC 1 1.008 0.0000 A 2.64953e-01 6.56888e-02
H1 1 1.008 0.0000 A 2.47135e-01 6.56888e-02
H2 1 1.008 0.0000 A 2.29317e-01 6.56888e-02
H3 1 1.008 0.0000 A 2.11499e-01 6.56888e-02
HA 1 1.008 0.0000 A 2.59964e-01 6.27600e-02
H4 1 1.008 0.0000 A 2.51055e-01 6.27600e-02
H5 1 1.008 0.0000 A 2.42146e-01 6.27600e-02
HO 1 1.008 0.0000 A 0.00000e+00 0.00000e+00
HS 1 1.008 0.0000 A 1.06908e-01 6.56888e-02
HW 1 1.008 0.0000 A 0.00000e+00 0.00000e+00
HP 1 1.008 0.0000 A 1.95998e-01 6.56888e-02
I 53 126.9 0.0000 A 4.18722e-01 1.67360e+00
Cl 17 35.45 0.0000 A 4.40104e-01 4.18400e-01
Na 11 22.99 0.0000 A 3.32840e-01 1.15897e-02
IB 0 131.0 0.0000 A 8.90899e-01 4.18400e-01
MG 12 24.305 0.0000 A 1.41225e-01 3.74342e+00
N 7 14.01 0.0000 A 3.25000e-01 7.11280e-01
NA 7 14.01 0.0000 A 3.25000e-01 7.11280e-01
NB 7 14.01 0.0000 A 3.25000e-01 7.11280e-01
NC 7 14.01 0.0000 A 3.25000e-01 7.11280e-01
N2 7 14.01 0.0000 A 3.25000e-01 7.11280e-01
N3 7 14.01 0.0000 A 3.25000e-01 7.11280e-01
N* 7 14.01 0.0000 A 3.25000e-01 7.11280e-01
O 8 16.00 0.0000 A 2.95992e-01 8.78640e-01
OW 8 16.00 0.0000 A 3.15061e-01 6.36386e-01
OH 8 16.00 0.0000 A 3.06647e-01 8.80314e-01
OS 8 16.00 0.0000 A 3.00001e-01 7.11280e-01
O2 8 16.00 0.0000 A 2.95992e-01 8.78640e-01
P 15 30.97 0.0000 A 3.74177e-01 8.36800e-01
S 16 32.06 0.0000 A 3.56359e-01 1.04600e+00
SH 16 32.06 0.0000 A 3.56359e-01 1.04600e+00
CU 29 63.55 0.0000 A 3.39967e-01 3.59824e-01
FE 26 55.00 0.0000 A 0.00000e+00 0.00000e+00
K 19 39.10 0.0000 A 4.73602e-01 1.37235e-03
Rb 37 85.47 0.0000 A 5.26699e-01 7.11280e-04
Cs 55 132.91 0.0000 A 6.04920e-01 3.37230e-04
; spc water - use only with spc.itp & settles
OW_spc 8 15.9994 0.0000 A 3.16557e-01 6.50629e-01
HW_spc 1 1.0080 0.0000 A 0.00000e+00 0.00000e+00
Li 3 6.94 0.0000 A 2.02590e-01 7.65672e-02
Zn 30 65.4 0.0000 A 1.95998e-01 5.23000e-02
;tip4p-EW
HW_tip4pew 1 1.008 0.0000 A 0.00000e+00 0.00000e+00
OW_tip4pew 8 16.00 0.0000 A 3.16435e-01 6.80946e-01
; tip4p
HW_tip4p 1 1.008 0.0000 A 0.00000e+00 0.00000e+00
OW_tip4p 8 16.00 0.0000 A 3.15365e-01 6.48520e-01
;tip5p
HW_tip5p 1 1.008 0.0000 A 0.00000e+00 0.00000e+00
OW_tip5p 8 16.00 0.0000 A 3.12000e-01 6.69440e-01
; dummy defs
; MW=Dummy mass for tip4p/EW/5p water extra point charge
MW 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00
; Dummy masses for rigid CH3 and NH3 groups
MCH3 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00
MNH3 0 0.0000 0.0000 A 0.00000e+00 0.00000e+00
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