The force field suggestion critically depends on the type of protein RNA
complex you have and properties of the used starting structure.
For protein/RNA complex, use rather the SPC/E water model, unless
you have disordered system.
For prot/RNA we have generally better experience with ff12SB than with
ff14SB protein ff, noted in several our papers.
If you have binding of unstructured ssRNA, consider this:
Spontaneous binding of single-stranded RNAs to RRM proteins visualized by
unbiased atomistic simulations with a rescaled RNA force field.
10.1093/nar/gkac1106.
If you would like to see how difficult prot/RNA simulations could
be, see this: 10.1021/acs.jpcb.2c06168; there are also some suggestions
how to get the system under control (CUFIX by Aleksei Aksimentiev,
HBfix for selected interface H-bonds, etc).
Best wishes, Jiri
-------------------------------------------------------
Jiri Sponer
Institute of Biophysics of the Czech Academy of Sciences
Kralovopolska 135
CZ-61265 Brno
Czech Republic
e-mail: sponer.ncbr.muni.cz
http://www.ibp.cz/
https://www.ibp.cz/en/research/departments/structure-and-dynamics-of-nucleic-acids/info-about-the-department
-----------------------------------------------------------
On Wed, 28 Aug 2024, Reza Khayat via AMBER wrote:
> Hi,
> I'm likely wrong, but the mentioned tutorial uses leaprc.RNA.OL3 force field. This FF parameterizes RNA only. The protein requested information is lacking.
>
> Perhaps try the CUFIX: Non-bonded fix:
> https://bionano.physics.illinois.edu/CUFIX
>
> Best wishes,
> Reza
> ________________________________
> From: Guberman-Pfeffer, Matthew via AMBER <amber.ambermd.org>
> Sent: 27 August 2024 10:19 PM
> To: Debarati DasGupta <debarati_dasgupta.hotmail.com>; AMBER Mailing List <amber.ambermd.org>
> Subject: [EXTERNAL] Re: [AMBER] Protein RNA complex simulation best standards in the field.
>
> Hi Debarati,
>
> You may find this tutorial helpful from the great folks in the York group: https://urldefense.proofpoint.com/v2/url?u=https-3A__ambertutorials-2Drutgerslbsr-2Dc744272d5a9c1169e0dc9e19b8d800019105.gitlab.io_workshop_02-5FintoMD_MTR1_Build-5FMTR1.html&d=DwIGaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=S8Z3cXP5i4EsnWlDb2xN6NMoWY9LowF7xH5fKyUCyLlbCpzyeN0n2xpWKW1kSNYs&s=NUn84ejGdBUh59qVXi0HFqNt1nB8aQOsi8OvQKnzIEI&e=
>
> Best,
> Matthew
>
> On Aug 27, 2024, at 7:16 PM, Debarati DasGupta via AMBER <amber.ambermd.org> wrote:
>
> Hi all,
> I am trying to gain some insights on how best to proceed with some protein RNA complex simulations. What forcefields are recommended? I am assuming we have to use either ff14SB or 19SB as the RNA-OL3 can only parametrize RNA bases? Any ideas/suggestions. Do's and Don'ts will be much appreciated.
>
>
> Thanks
> Debarati
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Received on Wed Aug 28 2024 - 06:00:05 PDT
