Re: [AMBER] Terminal phosphates with RNA

From: Piia Bartos via AMBER <>
Date: Wed, 22 Feb 2023 18:46:38 +0000

Dear Prof Case,

Thanks for the quick response.

I have visualized the trajectories, and the issue is that the oxygens start to stretch away from the phosphate, and the phosphate also moves away from the rest of the RNA. This is usually visible on the last frame I can visualize in VMD without VMD crashing.

The protein is most likely not affecting the issue, as this is clearer at the 5' end that is not bound to the protein but is facing the solvent (there are 2 RNA chains). I will check tomorrow with just the RNA chains.


Piia Bartoš, Ph.D. (Pharmacy)
Project Researcher
University of Eastern Finland | UEF | School of Pharmacy
Kuopio Campus | Canthia
Yliopistonranta 1 C | P.O. BOX 1627 | 70211 Kuopio
+358 50 548 8376 |<>
From: David A Case <>
Sent: Wednesday, February 22, 2023 17:14
To: Piia Bartos <>; AMBER Mailing List <>
Subject: Re: [AMBER] Terminal phosphates with RNA
On Wed, Feb 22, 2023, Piia Bartos via AMBER wrote:
>I am trying to simulate an RNA-protein complex where I need the parameters
>for 5' terminal phosphates. I know of terminal_monophosphate.lib and
>terminalphos.LJbb-RNA.lib, which should contain these parameters for the
>corresponding force fields.
>The problem is that these simulations crash because of the phosphates
>become unstable, after a few ns of the production run. My default settings
>include ff19SB for protein, OL3 for RNA and OPC water model, and HMR to use
>4fs timestep.
Can you say what you mean by "the phosphates become unstable"?  Are close
contacts formed between the terminal phosphate and some other group?
I don't think there is any fundamental problem with the paramters -- I have
run many simulations that appeared to be fine.  But that doesn't mean that
these parameters are always good.  You need to find out what is going wrong
-- a simple visualization of the trajectory is the best first step.  If the
problem involves the protein, that is probably very system-dependent.
One point: be sure that you system really has a single phosphate at the 5'
terminus, and you are not just trying to simulate what some crystallographer
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Received on Wed Feb 22 2023 - 11:00:03 PST
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