Dear David:
Thanks very much for your replay!
Substituting sulfur for selenium and then hand-edit the files to move S back to Se
Maybe this is a good solutions for this systems, but I still have a question:
As described in AMBER 2016 Manual (Page 145):"QM/MM calculations without link atoms require mass, charges, van der Waals and GB radii in the prmtop
file. All bonds, angles, and dihedrals parameters involving QM atoms are neglected. In the case of electrostatic embedding the charges are also neglected."
Is this sentence means that mass, van der Waals and GB radii are requried for both QM and MM regions?
If so, "hand-edit the files to move S back to Se" should change the mass, van der Waals and GB radii of S back to Se. Where can I get these correct parameters.
I dont konw my understanding is correct or not.
Looking forward to your replay again.
Best wishes!
At 2017-03-15 22:19:25, "David Case" <david.case.rutgers.edu> wrote:
>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 - 19:00:02 PDT
