On Mon, Oct 24, 2022, Sara Mahmoud via AMBER wrote:
>Dear all,
>
>I have a question regarding the 12-6-4 lj nonbonded model of the metal.
>
>I don't understand how in this tutorial they defined
>new terms for NAMG, NGMG, OPMG. And why exactly the N7 from adenine and
>guanine were selected?
>My system is a protein, should I add new terms for the ligating residues?
>or only run parmed command without introducing new terms?
The tutorial is looking at nucleic acids, where there might be specific
setups for interactions with N7 of the bases, or with the phosphate oxygen
of the backbone. Neither of these are present in proteins, so you should
not need that complication.
....dac
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Received on Mon Oct 24 2022 - 06:00:03 PDT
