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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>>
>
>
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Received on Fri Oct 11 2024 - 10:00:02 PDT
