On Thu, Apr 10, 2025, ηδΈη via AMBER wrote:
>
>I am planning to perform constant-pH molecular dynamics simulations (CPHMD)
>using AMBER 2022 to study DNA behavior in solution.
>
>From the documentation, I understand that certain residues require
>name changes to reflect protonation states (e.g., ASP β AS4 at
>pH 7). Could you clarify how DNA bases should be renamed in such
>simulations? Specifically:
>
> 1. For adenine and Cytosine (currently "DA" and "DC" in standard
> residues), what should its nomenclature be at pH 7?
>
> 2. Are there standardized naming rules for other DNA bases (e.g.,
> cytosine, guanine, thymine) under constant-pH conditions?
I don't know the answers to your questions. The protonated residues are in
the file $AMBERHOME/dat/leap/lib/all_prot_nucleic10.lib, but there are no
comments there. You might be able to figure things out by looking at these
structures, and picking the one(s) that correspond to your situation.
But, the Amber Reference Manual (section 26.2) talks only about proteins,
and is pretty silent about DNA. I'm hoping that my repeating this question
will inspire someone the list who knows about constant pH for nucleic acids
to chime in.
....dac
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Received on Mon Apr 14 2025 - 11:00:02 PDT
