On Thu, Oct 10, 2024, Maciej Spiegel via AMBER wrote:
>
>I would like to check how chirality affects the binding between two DNA
>strands. How can I enforce a specific chirality? Should I reparametrize
>both the S and R conformers, or is it possible to handle this during the
>simulation?
Can you say more about which "specific chirality" you have in mind here?
For proteins (as an example) switching between L and D-amino acids (changing
chirality at the Calpha position) doesn't require any new parameterization.
I don't recall any corresponding discussions about DNA, but it is entirely
possible that something similar happens there.
As for "enforcing chirality": If you have a reasonable starting structure,
with the chirality you want, it will probably not flip upon the usual
minimization or MD protocols. You can make sure by using the makeCHIR_RST
script in AmberTools, which will add restraints to prevent chirality
flipping. [Just beware: this is a script to *maintain* an existing
chirality; it is not a tool to transform between conformers.[
...good luck...dac
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Received on Thu Oct 10 2024 - 16:00:04 PDT
