[gmx-users] Atoms in the .top are not numbered consecutively from 1

[Jennifer Vo]

Dear All,
I have got this error after running grompp
Fatal error:
Atoms in the .top are not numbered consecutively from 1 (rather, atomnr =
4, while at->nr = 2)

My topology file is
; Include forcefield parameters
#include "gromos54a7.ff/forcefield.itp"

; Include ligand topology
#include "nap_uniatom.itp"

; Include water topology
#include "gromos54a7.ff/spc.itp"
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif
[ system ]
; Name
NAP in water
[ molecules ]
; Compound        #mols
NAP                   1
SOL              2654

The I checked the file "nap_uniatom.itp" and it start from Atom 1,
NAP
 8026
    1NAP    O3X    1   2.599   2.617   1.841
    1NAP   HOP3    2   2.518   2.642   1.886
    1NAP    P2B    3   2.654   2.469   1.866
    1NAP    O1X    4   2.628   2.363   1.772
    1NAP    O2B    5   2.580   2.447   2.009
    1NAP    O2X    6   2.802   2.504   1.908
    1NAP   HOP2    7   2.817   2.591   1.946

Could you please tell me where is the problem from and a possible solution?
 Many thanks in advance.
Regards,
Jennifer