[gmx-users] exclusions in topological file

[jozef hritz]

Can somebody help me, how to exclude non-bonded interaction between
non-bonded atoms? 
Only for testing syntax I created system containing 2 non-bonded 
ZN atoms (1,2) in the distance 2 A (pdb, gro and top files are below). 
I made for it guite large box and tried to exclude non-bonded 
interaction between them in top file, by writing

[ exclusions ]
  1  2

but after runing grompp it wrote me:

Warning 1 [file "zin.top", line 19]:
    Invalid order in directives exclusions
Excluding 1 bonded neighbours for Protein 1

I don't understand what invalid order in exclusion I made and why it
excluded bonded neighbours when system contains only two non-bonded
ZN atoms.
By runing mdrun it's clear there is big repulsion between atoms.  

 	Thank You very much for help
 
 							Jozef
 
 zin.pdb:  
 
HETATM    1  ZN  ZN      1       0.000   0.000   0.000
HETATM    2  ZN  ZN      2       0.200   0.000   0.000
 
 
 
 gro file:
 
Gnomes, ROck Monsters And Chili Sauce
    2
    1ZN      ZN    1   0.000   0.000   0.000
    2ZN      ZN    2   0.200   0.000   0.000
   1.0000   1.00000   1.00000
 
 
 top file
 
#include "ffgmx.itp"

[ moleculetype ]
; Name            nrexcl
Protein             3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB      massB
     1     ZN      1     ZN     ZN      1          2      65.37   ; qtot 2
     2     ZN      2     ZN     ZN      2          2      65.37   ; qtot 4

[ exclusions ]     ; how to exclude nonbonded interaction between 1 and 2?
;  ai    aj
    1     2

; Include Position restraint file
#ifdef POSRES
#include "zin.itp"
#endif

; Include water topology
#ifdef FLEX_SPC
#include "flexspc.itp"
#else
#include "spc.itp"
#endif

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

[ system ]
; Name
Protein

[ molecules ]
; Compound        #mols
Protein             1