Hi Anthony,
>
> I'm attempting to parameterise 4 calcium ions and 2 zinc ions in a metalloprotease. The last time I parameterised metal for a protein was quite a few years ago and I did it by writing my own 2nd derivative of the Hessian-based model using a Gaussian log file. Unfortunately, I don't have access to a Gaussian license anymore. I've requested a GAMESS-US license, but I've never used that before.
>
For the Ca2+ ions, a nonbonded model would be a suitable choice. For Zn2+ ions, you can use the bonded model. You can check this webpage for more information about the difference between the bonded model and nonbonded model: https://ambermd.org/tutorials/advanced/tutorial20/index.php <https://ambermd.org/tutorials/advanced/tutorial20/index.php>.
> Are there any empirical calculations I can perform to derive force constants? To satisfy charges I believe I can still use the RED server.
>
Yes, for Zn2+, there is an option 2e for step 2, which corresponds to an empirical method to derive the force constants for Zn2+ containing systems: https://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00773 <https://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00773>.
Hope it helps,
Pengfei
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Received on Thu Jul 22 2021 - 19:30:02 PDT
