Dear Amber community,
Ken Merz has recently (Feb 4, 2021) published monovalent ion parameters specific for the OPC3, OPC, TIP3P-FB, and TIP4P-FB water models: https://doi.org/10.1021/acs.jcim.0c01390
However, it appears that these parameters differ from the frcmod files included in Amber, frcmod.ions1lm_126_hfe_opc and frcmod.ions1lm_126_iod_opc. Presumably, these parameters were derived in the same way as the parameters for other water models described in
https://doi.org/10.1021/ct500918t, but neither the manual nor the frcmod files provide a reference. However, it seems like the methodology to derive the parameters is similar between these two publications, so I don't understand why the frcmod parameters are different from the recently published ones.
Does anyone in the community know the source for the parameters in the Amber frcmod files? In particular, is the 2015 JCTC paper from Li, Song, & Merz the correct reference for these frcmod files?
Best,
Chapin Cavender
PhD student, Dave Mathews lab
Department of Biochemistry & Biophysics
University of Rochester School of Medicine & Dentistry
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Message: 1
Date: Mon, 25 Jan 2021 15:35:11 -0500
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Subject: Re: [AMBER] OPC monovalent ion parameters
To: AMBER Mailing List <amber.ambermd.org>
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I'd check this:
Developing Monovalent Ion Parameters for the Optimal Point Charge (OPC)
Water Model
Daniel E Clark John C Dood Brent P Krueger
https://urldefense.proofpoint.com/v2/url?u=https-3A__doi.org_10.1096_fasebj.31.1-5Fsupplement.761.24&d=DwICAg&c=4sF48jRmVAe_CH-k9mXYXEGfSnM3bY53YSKuLUQRxhA&r=E2G_FiEtGhStTPYmNtsKk1lRtqjn8haGVq3W8F23rEPZ9zK1SwNK3Gk-rV9NMQ5E&m=tEy6OOqSZ9EMJPKqXZkDwCJFyjHeHwlzTz1O1Njnmuw&s=FaaSRVDO8kO3GYMmdMBF9F65ne0UFzGUdTeKAxbkjFs&e=
On Mon, Jan 25, 2021 at 1:07 PM Sebastian Oleksy <so389.chem.rutgers.edu>
wrote:
> Hello,
>
> I will be running MD simulations on a nucleic acid system, using the
> 4-site OPC water model in combination with the RNA.OL3 force field. I was
> wondering what specific monovalent ion parameters would be best to use here
> ? Li/Merz 12-6 HFE set, 12-6 IOD set, or even J/C_tip4pew? Others? Or would
> perhaps OPC3 be better than the 4-site OPC model for this? If anyone has
> any experience or guidance, it would be much appreciated. Thank you.
>
> Respectfully,
> Sebastian Oleksy
>
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Received on Sat Feb 13 2021 - 12:00:02 PST
