On Wed, Mar 15, 2017, 杨满意 wrote:
> I have a question in how to generate input files (.prmtop and
> .inpcrd) for my QM/MM MD simulation with Amber16.
> the QM reagion: C6H5ISe (where I and Se have no force field
> parameters in GAFF)
> the MM reagion : C6H6
Amber requires an MM force field, even for QM parts. You can use inaccurate
or made-up parameters there, but they must be present. In your case, this
probably means learning enough about libraries and file formats to create
something by hand.
I'm not sure what "C6H5ISe" looks like, so I can't offer much advice, but
try this: use antechamber to create a library for C6H5IS (substituting
sulfur for selenium; iodine is indeed present in gaff and gaff2). Then
hand-edit the files to move S back to Se.
...good luck....dac
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Received on Wed Mar 15 2017 - 07:30:03 PDT
