Let’s say, I am interested in phosphorothioate linkages, particularly to compare Rp with Sp from here: https://ars.els-cdn.com/content/image/3-s2.0-B9780080977423006182-f0600618-14-9780080977423.jpg <https://ars.els-cdn.com/content/image/3-s2.0-B9780080977423006182-f0600618-14-9780080977423.jpg>
–
Maciej Spiegel, MPharm PhD
assistant professor
.GitHub <
https://farmaceut.github.io/>
Department of Organic Chemistry and Pharmaceutical Technology,
Faculty of Pharmacy, Wroclaw Medical University
Borowska 211A, 50-556 Wroclaw, Poland
> Wiadomość napisana przez Carlos Simmerling <carlos.simmerling.stonybrook.edu> w dniu 11.10.2024, o godz. 12:06:
>
> Indeed, there are many chiral centers in a nucleotide- which do you mean?
>
> On Thu, Oct 10, 2024, 6:49 PM David A Case via AMBER <amber.ambermd.org <mailto:amber.ambermd.org>> wrote:
> 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 Fri Oct 11 2024 - 10:00:02 PDT
