Are you using explicit water? If so, there should be an ions frcmod file
appropriate for the water model. If not, maybe there's a non-hydrated
ions frcmod file. This should be explained in docs somewhere, try
searching on 'amber frcmod ions'.
Bill
On 11/3/19 3:11 AM, student_cbc_1 nnlab wrote:
> Respected sir,
>
> We plan to run classical MD simulation of α-cyclodextrin with iodine and
> iodide (I-) ion. However, following error appears when the .prmtop and
> .inpcrd are attempted to be generated. We plan to use ff10 force field
> Amber11, where parameter of iodide (I-) ion is given. The parameters of
> α-cyclodextrin and iodine are prepared using antechamber. The following
> message appears when *the .prmtop and .inpcrd are attempted to be
> generated.*
>
>> saveamberparm x acd.prmtop acd.inpcrd
> Checking Unit.
>
> WARNING: The unperturbed charge of the unit: -3.001000 is not zero.
>
> -- ignoring the warning.
>
> Building topology.
>
> Building atom parameters.
>
> For atom: .R<I- 5>.A<I- 1> Could not find type: I-
>
> For atom: .R<I- 6>.A<I- 1> Could not find type: I-
>
> For atom: .R<I- 7>.A<I- 1> Could not find type: I-
>
> Parameter file was not saved.
>
>
> I look forward for the possible solution to the above problem, please.
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Received on Sun Nov 03 2019 - 04:00:03 PST
