I don't have good suggestions for parameter development for Au, but I would
have concerns over using GB for something like Au. MM-PBSA might be a
better option and has fewer empirical parameters to worry about.
On Mon, Aug 9, 2021 at 10:15 AM Matthew Guberman-Pfeffer <
matthew.guberman-pfeffer.uconn.edu> wrote:
> Dear Amber Community,
>
> MM-GBSA is returning a “bad atom type” error because my system includes Au
> atoms— I’m looking at a protein-Au surface system, and previously, the
> below publication used the MM-GBSA approach to assess initial
> protein-surface docking poses (
> https://pubs.acs.org/doi/abs/10.1021/acs.jpclett.5b02746 <
> https://pubs.acs.org/doi/abs/10.1021/acs.jpclett.5b02746>).
>
> I know how to add the parameters to the mdread2.f90 file and how to
> recompile the code afterwards. I just don’t know where I can find the
> appropriate parameters, or how I can compute them, for Au. I’d greatly
> appreciate any suggestions.
>
> Best,
> Matthew
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Received on Wed Aug 11 2021 - 16:30:03 PDT
