I don't see iodide (I- atom type) in the dat/leap/parm/parm10.dat file.
Instead I see iodine, which you said you needed to prepare using
antechamber. perhaps you switched the two?
I 126.9 4.690 iodine (Applequist) (not iodide!)
On Sun, Nov 3, 2019 at 6:11 AM student_cbc_1 nnlab <
studentcbcnnlab.gmail.com> 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 - 05:00:01 PST
