Dear Maciej,
> 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>
You can use REDServer Dev./PyRED for that...
See
https://upjv.q4md-forcefieldtools.org/Tutorial/Tutorial-4.php#V3
You just replace dimethylphosphate by dimethylthiophosphate and run
the job with the 4...n nucleosides.
As you introduce a new chiral center at the P atom you may want to use
2 different dimethylthiophosphate - I mean a S atom instead of O1P or
a S atom instead of O2P (you end up with diastereoisomers i.e. R/S at
the P atom + 1R,3S,4R for DNA). You can also replace the O3' and O5'
atoms... You can run a single PyRED job for all these cases. You could
test the same approach with Selenium as well...
Best Francois
>> 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.[
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Received on Fri Oct 11 2024 - 14:30:02 PDT
