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

[Cuong Nguyen]

Thank you very much David

Cuong

On 18 February 2013 17:40, David van der Spoel <spoel at xray.bmc.uu.se> wrote:

> 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
> --
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