On Wed, Jan 07, 2026, Mandar Kulkarni via AMBER wrote:
...just to expand (a bit) on what Zhen alread said:
>
>I am curious if IOD parameters instead of CM are better for structural
>refinements of modeled RNAs? It is mentioned in the manual, but I could not
>find any citation in the context of nucleic acids.
See References 149 and 150 in the Amber 2025 Reference Manual for
RNA-specific suggestions. Further info below.
Be sure to study the "Metal Ion Binding Tutorial" (tutorial 2.4 at the Amber
Web site.) This is a wide-ranging tutorial, but for divalent ions
interacting with RNA, I recommend burrowing down to here:
https://ambermd.org/tutorials/advanced/tutorial20/12_6_4.php
(This is the tutorial that Zhen recommended.)
Then go down even further to Example B, for parameters particularly tuned to
RNA. Of course, as you can see, there are *many* possibilities that you
might consider; but the "Panteva et al." parameters certainly be on the list
of things you might try.
...good luck...dac
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Received on Wed Jan 07 2026 - 10:00:02 PST
