ARES PRIVATE
My email address is now .a-star.edu.sg. Kindly update your address book accordingly.
Hi Zhen,
Thanks for the clarification.
I am curious if IOD parameters instead of CM are better for structural refinements of modeled RNAs? It is mentioned in the manual, but I could not find any citation in the context of nucleic acids.
Thanks,
Mandar
From: Li, Zhen <lizhen6.chemistry.msu.edu>
Date: Thursday, 8 January 2026 at 12:27 AM
To: amber.ambermd.org <amber.ambermd.org>, Mandar Kulkarni <mandar_kulkarni.a-star.edu.sg>
Subject: Re: [AMBER] Mg2+ parameters: Optimized or CM
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Hi Mandar,
Thank you for being interested in using the Li-Merz Parameters for Mg2+.
To clarify, the Rmin/2 and epsilon parameters in Ref. 145 are not designed for 12-6 only. They must be used with the 12-6-4 model, as outlined in this tutorial<
https://ambermd.org/tutorials/advanced/tutorial20/12_6_4.php>. The intended C4 values are listed in Table 4 of Ref. 145.
If the parameter is used with the Joung-Cheatham Cl- parameter, then the Mg2+ CM set (from Ref. 144) should perform well. Hope it is clear.
Best regards,
Zhen.
_____________________
Zhen Li<
http://lizhen62017.wixsite.com/home>, Ph.D.,
The Merz Research Group<
http://merzgroup.org>,
Michigan State University,
Cleveland Clinic.
________________________________
From: Mandar Kulkarni via AMBER <amber.ambermd.org>
Sent: Wednesday, January 7, 2026 7:00 AM
To: amber.ambermd.org <amber.ambermd.org>
Subject: [AMBER] Mg2+ parameters: Optimized or CM
ARES PRIVATE
My email address is now @a-star.edu.sg. Kindly update your address book accordingly.
Dear AMBER developers,
I am reading the AMBER25 manual for ion parameter suggestions and noticed that Mg2+ CM parameters with TIP3P are cited from Ref. 145 (J. Chem. Theory Comput., 2014, 10, 289–297), and found them mentioned in Ref. 144 also (J. Chem. Theory Comput., 2013, 9, 2733–2748) .
Ref. 145 mentions different set of optimized parameters for Mg2+ (Rmin/2 = 1.437 and epsilon = 0.02257962), whereas CM parameters are (Rmin/2 = 1.360 and epsilon = 0.01020237).
Can developers confirm which set is correct for RNA simulations in TIP3P and Joung-Cheatham Cl- ions?
Also, is the IOD set from Ref. 144 better for equilibrating predicted RNA models?
Thanks,
Mandar
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Received on Wed Jan 07 2026 - 09:30:03 PST
