Good morning,
You can use this (old) tutorial as a starting point for running nucleic
acid simulations: https://ambermd.org/tutorials/basic/tutorial1/index.php
But, you *should* read the methods sections of the papers Darrin mentioned,
understand what is meant by eg., thermostat and barostat by looking up
those input file variables in the Amber manual, and set the variables
accordingly.
After I build & solvate my nucleic acid system, I personally use the
following script to minimize and solvent-equilibrate:
https://github.com/drroe/AmberMdPrep
Good luck!
-Christina
On Wed, Feb 21, 2024 at 4:44 PM Debarati DasGupta via AMBER <
amber.ambermd.org> 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>
>
> 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>
>
> 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
>
> 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
> These ion models reproduce very well a wide range of bulk properties:
> 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
> 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>)
> 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
> _______________________________________________
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--
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Christina Bergonzo
Research Chemist
Biomolecular Measurement Division, MML, NIST
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Received on Thu Feb 22 2024 - 06:00:02 PST
