/usr/share/gromacs/top/amber99.ff/tip5p.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 | [ moleculetype ]
; molname nrexcl
SOL 2
[ atoms ]
; id at type res nr res name at name cg nr charge mass
1 OW_tip5p 1 SOL OW 1 0 16.00000
2 HW_tip5p 1 SOL HW1 1 0.241 1.00800
3 HW_tip5p 1 SOL HW2 1 0.241 1.00800
4 MW 1 SOL LP1 1 -0.241 0.00000
5 MW 1 SOL LP2 1 -0.241 0.00000
#ifndef FLEXIBLE
[ settles ]
; i funct doh dhh
1 1 0.09572 0.15139
#else
[ bonds ]
; i j funct length force.c.
1 2 1 0.09572 502416.0 0.09572 502416.0
1 3 1 0.09572 502416.0 0.09572 502416.0
[ angles ]
; i j k funct angle force.c.
2 1 3 1 104.52 628.02 104.52 628.02
#endif
[ virtual_sites3 ]
; Vsite from funct a b c
4 1 2 3 4 -0.344908262 -0.34490826 -6.4437903493
5 1 2 3 4 -0.344908262 -0.34490826 6.4437903493
[ exclusions ]
1 2 3 4 5
2 1 3 4 5
3 1 2 4 5
4 1 2 3 5
5 1 2 3 4
; The positions of the vsites are computed as follows:
;
; LP1 LP2
;
; O
;
; H1 H2
;
; angle A (H1-O-H2) = 104.52
; angle B (M1-O-M2) = 109.47
; dist C (H-O) = 0.09572 nm
; dist D (M-O) = 0.070 nm
;
;atom x y z
;O 0.0 0.0 0.0
;H1 0.585882276 0.756950327 0.0
;H2 0.585882276 -0.756950327 0.0
;M1 -0.404151276 0.0 0.571543301
;M2 -0.404151276 0.0 -0.571543301
; Dummy pos x4 = x1 + a4*(x2-x1) + b4*(x3-x1) + c4*((x2-x1) x (x3-x1))
; Dummy pos x5 = x1 + a5*(x2-x1) + b5*(x3-x1) + c5*((x2-x1) x (x3-x1))
; a4 = b4 = a5 = b5 = (D*cos(B/2)) / (2*C*cos(A/2)) = -0.34490826
; c5 = -c4 = (D * sin(B/2))/ (C^2 * sin(A)) = 6.4437903
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