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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Received on Wed Feb 21 2024 - 14:00:02 PST
