On Thu, Mar 16, 2017, 杨满意 wrote:
>
> 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?
Yes.
> 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.
The mass needs to be the correct mass, and vdW parameters can probably be
estimated from the difference between S and Se. (Have you done the literature
search that I suggested? There are several force fields available that cover
the entire periodic table.) Unless you are using GB, dummy values can be
given for those.
...good luck...dac
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Received on Thu Mar 16 2017 - 06:00:04 PDT
