[AMBER] Terminal phosphates with RNA

From: Piia Bartos via AMBER <amber.ambermd.org>
Date: Wed, 22 Feb 2023 09:39:48 +0000


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.

Things I have tried:

  1. Removing terminal phosphates leads to stable simulations so the system is otherwise fine.
  2. Longer equilibration -> still crashes.
  3. Not using hydrogen mass repartitioning and 4fs timestep, but a timestep of 2fs -> still crashes.
  4. Using the OHE residue as described in Amber manual (3.2.3) and not -> still crashes.
  5. Changing the RNA force field to RNA.LJbb -> still crashes.

I am seeing some MC barostat warnings (MC Barostat: Decreasing size of volume moves) in the production run before the crash. Could it be that the parameters of these terminal phosphates are somehow incompatible with the MC barostat?

I would appreciate any help. I included my production script below.

Piia Bartos

# 500 ns production Langevin thermostat + Monte carlo barostat dynamics
   irest=1, ntx=5,
   ntpr=25000 ntwx=25000, ntwr=25000,
   ntb=2, barostat=2, cut=10, iwrap=1,

   nstlim=125000000, nscm=0, dt=0.004,
   ntt=3, gamma_ln = 1, ig=-1, temp0=310, tempi=310,
   ntc=2, ntf=2,
   netfrc = 0,
   skin_permit = 0.75,

Piia Barto¹, 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 | piia.bartos.uef.fi<mailto:piia.bartos.uef.fi>
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Received on Wed Feb 22 2023 - 02:00:03 PST
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