[gmx-users] ions.itp file for polarized ions

[Cuong Nguyen]

Dear Gmx-users,

I have ions.itp file for polarized Na+ and Cl- as follows:


; Sodium, Na+
[ moleculetype ]
; molname    nrexcl
Na+        1

[ atoms ]
; id    at type    res nr    residu name    at name    cg nr    charge
1    Nac    1    Na+        Nac1    1    +0.312403
2    Nas    1    Na+        Nas1    1    +0.687597

[ polarization ]
; See notes above.    alpha (nm^3)
1    2    1     0.00024

[ exclusions ]
; iatom excluded from interaction with i
1    2
2    1

; Chloride, Cl-
[ moleculetype ]
; molname    nrexcl
Cl-        1

[ atoms ]
; id    at type    res nr    residu name    at name    cg nr    charge
1    CLc    1    Cl-        CLc1    1    -4.457187
2    CLs    1    Cl-        CLs1    1    +3.457187

[ polarization ]
; See notes above.    alpha (nm^3)
1    2    1     0.00325

[ exclusions ]
; iatom excluded from interaction with i
1    2
2    1

and after running the command:

*grompp -f ions.mdp -o min.tpr -c box1.g96*

it appears the error:

Program grompp, VERSION 4.5.5
Source code file: topio.c, line: 656

Fatal error:
Syntax error - File ions.itp, line 20
Last line read:
'[ exclusions ]'
Invalid order for directive exclusions

Please help me to deal with this issue?

Thanks a lot in advance.

Best regards,

Cuong