Urea topology problem

eq.mdp

integrator = md
dt = 0.00002

nsteps = 60000
nstxout = 0
nstvout = 0
nstlog = 50
nstenergy = 50
nstxtcout = 50

vdw-type = cut-off
rlist = 0.9
coulombtype = pme
rcoulomb = 0.9

rvdw = 0.9
; dispcorr = enerpres ; Not sure about disp corrections...

tcoupl = v-rescale
tc-grps = System
ref_t = 300
tau_t = 0.1

pcoupl = berendsen
compressibility = 4.5e-5
ref_p = 1.0
;pcoupltype = anisotropic
;compressibility = 4.5e-5 4.5e-5 4.5e-5 0.0 0.0 0.0
;ref_p = 1.0 1.0 1.0 0.0 0.0 0.0

;gen_vel = yes
;gen_temp = 300
 constraints = none 
;constraints = all-bonds
;constraints = all-angles

topol.top

[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1          2         no        0.5      0.5

[ atomtypes ]
H H 1 1.00794 0.333 A 0.0 0.0
C C 6 12.0107 0.142 A 0.004886848836 1.358954496e-05
O O 8 15.9994 -0.39 A 0.0023639044 1.58986881e-06
N N 7 14.0067 -0.542 A 0.003352757409 3.95095129e-06

[ moleculetype ]
URE 1
[ atoms ]
1 N 1 URE N1 1 -0.542
2 C 1 URE C2 1 0.142
3 O 1 URE O3 1 -0.39
4 N 1 URE N4 1 -0.542
5 H 1 URE H5 1 0.333
6 H 1 URE H6 1 0.333
7 H 1 URE H7 1 0.333
8 H 1 URE H8 1 0.333
[ bonds ]
1 2 1 0.135 10300000.0
2 3 1 0.1265 13100000.0
2 4 1 0.135 10300000.0
1 5 1 0.1 18700000.0
1 6 1 0.1 18700000.0
4 7 1 0.1 18700000.0
4 8 1 0.1 18700000.0
[ angles ]
2 1 5 1 120.0 390
2 1 6 1 120.0 390
5 1 6 1 120.0 445
1 2 3 1 121.4 690
1 2 4 1 117.2 636
3 2 4 1 121.4 690
2 4 7 1 120.0 390
2 4 8 1 120.0 390
7 4 8 1 120.0 445
[ dihedrals ]
4 7 8 2 2 0.0 0.051
1 5 6 2 2 0.0 0.051
2 1 4 3 2 0.0 0.051
[ dihedrals ]
3 2 1 5 1 180.0 41.8 2
3 2 4 8 1 180.0 41.8 2
[ system ]
Generated by chemlab
[ molecules ]
URE 1

urea.gro

Generated by chemlab
    8
    1URE     N1    1   0.117  -0.062  -0.000
    1URE     C2    2   0.000   0.005  -0.000
    1URE     O3    3   0.000   0.127   0.000
    1URE     N4    4  -0.117  -0.062  -0.000
    1URE     H5    5   0.201  -0.014  -0.000
    1URE     H6    6   0.117  -0.159   0.000
    1URE     H7    7  -0.117  -0.159  -0.000
    1URE     H8    8  -0.201  -0.014   0.000
   2.00000   2.00000   2.00000