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

[David van der Spoel]

On 2013-02-18 10:16, Cuong Nguyen wrote:
> 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?
remove the exclusions. Since there are no bonds you can not have 
exclusions. Exclusions will nevertheless be generated. Please check the 
topology using gmxdump.
>
> Thanks a lot in advance.
>
> Best regards,
>
> Cuong
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se