[gmx-users] ERROR when generated a rtp file with "grompp"

[ookami a]

Dear all:

I have such error below:

Fatal error:
number of coordinates in coordinate file (p_wateroil.gro, 55383)
             does not match topology (topol.top, 55421)

it tells that the number of atoms are not same.
In my top file:
 [ molecules ]
; Compound        #mols
Protein_chain_A     1
DOD               780
SOL              7882

I have 1*2097 + 780*38 + 7882*3 = 55383 atoms which suppose to be same in
the .gro file.

If I modified my top to
[ molecules ]
; Compound        #mols
Protein_chain_A     1
DOD               779
SOL              7882

it generate such errors :
Warning: atom name 1 in topol.top and p_wateroil.gro does not match (C1 - N)
Warning: atom name 2 in topol.top and p_wateroil.gro does not match (H11 -
H1)
Warning: atom name 3 in topol.top and p_wateroil.gro does not match (H12 -
H2)
Warning: atom name 4 in topol.top and p_wateroil.gro does not match (H13 -
H3)
Warning: atom name 5 in topol.top and p_wateroil.gro does not match (C2 -
CA)
Warning: atom name 6 in topol.top and p_wateroil.gro does not match (H21 -
HA)
Warning: atom name 7 in topol.top and p_wateroil.gro does not match (H22 -
CB)
Warning: atom name 8 in topol.top and p_wateroil.gro does not match (C3 -
HB1)
Warning: atom name 9 in topol.top and p_wateroil.gro does not match (H31 -
HB2)
Warning: atom name 10 in topol.top and p_wateroil.gro does not match (H32 -
HB3)
Warning: atom name 11 in topol.top and p_wateroil.gro does not match (C4 -
C)
Warning: atom name 12 in topol.top and p_wateroil.gro does not match (H41 -
O)
Warning: atom name 13 in topol.top and p_wateroil.gro does not match (H42 -
N)
Warning: atom name 14 in topol.top and p_wateroil.gro does not match (C5 -
CD)
Warning: atom name 15 in topol.top and p_wateroil.gro does not match (H51 -
HD1)
Warning: atom name 16 in topol.top and p_wateroil.gro does not match (H52 -
HD2)
Warning: atom name 17 in topol.top and p_wateroil.gro does not match (C6 -
CG)
Warning: atom name 18 in topol.top and p_wateroil.gro does not match (H61 -
HG1)
Warning: atom name 19 in topol.top and p_wateroil.gro does not match (H62 -
HG2)
Warning: atom name 20 in topol.top and p_wateroil.gro does not match (C7 -
CB)
(more than 20 non-matching atom names)

WARNING 1 [file topol.top, line 19983]:
  2053 non-matching atom names
  atom names from topol.top will be used
  atom names from p_wateroil.gro will be ignored

Anyone knows why and how to fix it?
Thank you!