Hi Debarati,
Sure! I'll put together some input files and scripts for you and send
to you directly.
best wishes,
Darrin
On 2/21/24 16:44, Debarati DasGupta wrote:
> Hello Darrin,
>
> thank you for your kind words and positivity.
> Would you be willing to send a few input files to test a run? I would
> appreciate if you may provide a leap.in and a minimization +
> equilibration input file.
> It would be great to have some reference accessible when I am drafting
> the setup from scratch.
>
> Thank you so much.
> Debarati
> ------------------------------------------------------------------------
> *From:* Darrin York via AMBER <amber.ambermd.org>
> *Sent:* Tuesday, January 30, 2024 6:32 AM
> *To:* amber.ambermd.org <amber.ambermd.org>
> *Subject:* Re: [AMBER] Best practises for running MD with RNA structures
> Hi Debarati!
>
> Welcome to the RNA structure and dynamics world! ;)
>
> As you know - nucleic acids acids are inherently charged systems so you
> will need to be careful to include the right solvation environment
> including necessary divalent metal ions, counterions and coions at the
> relevant concentrations (and with the right parameters), and equilibrate
> the environment quite a bit more than you might for a typical protein
> system (at least this is what we do).
>
> The methods sections of the following recent papers give a good summary
> of how we build and relax your systems:
>
> Ekesan, Nucleic Acids Res. (2019) 47, 10282-10295
> https://academic.oup.com/nar/article/47/19/10282/5568213
> <https://academic.oup.com/nar/article/47/19/10282/5568213>
>
> <https://academic.oup.com/nar/article/47/19/10282/5568213
> <https://academic.oup.com/nar/article/47/19/10282/5568213>>
>
> McCarthy, Nucleic Acids Res. (2023) 51, 4508–4518
> https://academic.oup.com/nar/article/51/9/4508/7127216
> <https://academic.oup.com/nar/article/51/9/4508/7127216>
>
> <https://academic.oup.com/nar/article/51/9/4508/7127216
> <https://academic.oup.com/nar/article/51/9/4508/7127216>>
>
> For monovalent ions; e.g., NaCl or similar we tend to use the models of
> Joung and Cheatham (there are different parameters sets that are
> designed to work optimally with different water models, and avoid
> "salting out" effects that plagued previous models):
> https://pubs.acs.org/doi/10.1021/jp8001614
> <https://pubs.acs.org/doi/10.1021/jp8001614>
>
> For divalent metal ions, we are a big fan of the 12-6-4 models of Li and
> Merz: https://pubs.acs.org/doi/10.1021/ct400751u
> <https://pubs.acs.org/doi/10.1021/ct400751u>
> These ion models reproduce very well a wide range of bulk properties:
> https://onlinelibrary.wiley.com/doi/10.1002/jcc.23881
> <https://onlinelibrary.wiley.com/doi/10.1002/jcc.23881>
> but it is critical in the case of interactions with RNA that the
> specific pairwise corrections of Panteva et al. are used:
> https://pubs.acs.org/doi/10.1021/acs.jpcb.5b10423
> <https://pubs.acs.org/doi/10.1021/acs.jpcb.5b10423>
> These corrections fine tune the divalent metal ion [Mg(II), Mn(II),
> Zn(II) and Cd(II)] interactions with nucleic acid binding sites for
> proper balanced interactions with water that are oftentimes essential
> for structure and/or function. Here's the tutorial (
> https://ambermd.org/tutorials/advanced/tutorial20/12_6_4.php
> <https://ambermd.org/tutorials/advanced/tutorial20/12_6_4.php>
>
> <https://ambermd.org/tutorials/advanced/tutorial20/12_6_4.php
> <https://ambermd.org/tutorials/advanced/tutorial20/12_6_4.php>>)
>
> that might help with that.
>
> Feel free to reach out if you would like to talk more.
>
> best wishes,
>
> Darrin
>
> On 1/29/24 17:53, Debarati DasGupta via AMBER wrote:
> > Hi all
> > I am new to the RNA structure world and interested to run some short
> MD On RNA structures.
> > Anyone may please point me out to a publication I can follow? Best
> practises sort of? Solvents? modified bases? Forcefields?
> > Any guidance on this would be deeply appreciated
> >
> > Debarati
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> <http://lists.ambermd.org/mailman/listinfo/amber>
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Received on Fri Feb 23 2024 - 13:30:02 PST
