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.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Nov 03 2019 - 03:30:01 PST
