On Sun, Nov 03, 2019, student_cbc_1 nnlab wrote:
>
>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.*
Iodide ion is part of the standard monatomic ions supported by Amber.
As Bill noted, these are water-model-specific, that is, they have been
optimized for use with a particular water model. You can get them
by "source leaprc.water.xxxx", where xxxx is your chosen water model.
Note the ff10 is in the "oldff" (old force field) folder for a reason:
there are times when users wish to reproduce an old calculation, or
just examine what parameters were used nine years ago. But none of
these should be used for current calculations.
...good luck....dac
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Received on Sun Nov 03 2019 - 05:00:02 PST
