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 - 05:30:02 PDT
