Hello Maciej.
For phosphothioate backbone, there are several (equivalent) parameters
you can use - the one from Orozco's group:
-
https://academic.oup.com/nar/article/51/10/4713/7143238
the parameters from the Sponer group:
-
https://pubs.acs.org/doi/full/10.1021/acs.jpcb.0c10192
and the parameters from the Matsson group:
-
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11127634/
I dont think there are parameters available for the other two analogs
the use an S atom as the linker between nucleotides.
Hope that helps!
Rodrigo.
On Fri, Oct 11, 2024 at 10:45 AM Carlos Simmerling via AMBER
<amber.ambermd.org> wrote:
>
> I am not aware of any parameters for these modifications being part of the
> standard force fields included with Amber, though I am not an expert in
> that area. Maybe it would help to update the email subject so it is clear
> that it is related to this phosphorothioate modification, and then people
> with more knowledge in that area may look at the email.
>
>
> On Fri, Oct 11, 2024 at 12:33 PM Maciej Spiegel <maciej.spiegel.umw.edu.pl>
> wrote:
>
> > 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
> >
> > –
> > 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>
> > 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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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
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