Hi Kendall,
Thank you for being interested in ZAFF. As you might have noticed here. ZAFF is a very exhaustive force field that covers all possible combinations of Zn2+ ligands in a specific forcefield.
To my knowledge today. There has not been a complete re-parametrization or ZAFF in ff19SB and OPC water. So, to be safe, I still suggest using ff14SB and TIP3P at this moment. Currently, there is not restriction to stop you from using ff19SB + OPC + ZAFF, but as you have mentioned, it sounds like putting new wine to an old bag.
We are glad to help if you could DM us the system that you are interested or any error message that you have encountered.
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: Cherry, Kendall via AMBER <amber.ambermd.org>
Sent: Monday, July 14, 2025 3:29 PM
To: amber.ambermd.org <amber.ambermd.org>
Subject: Re: [AMBER] Choice of protein/water force fields with ZAFF zinc parameters?
Sorry, just noticed a typo – I meant to say that the tutorial uses ff14SB and TIP3P.
Kendall Cherry
From: Cherry, Kendall <kche.email.unc.edu>
Date: Monday, July 14, 2025 at 3:25 PM
To: amber.ambermd.org <amber.ambermd.org>
Subject: Choice of protein/water force fields with ZAFF zinc parameters?
Hello AMBER community,
I am running simulations of a zinc finger protein and am planning to use ZAFF parameters to facilitate the Zn parametrization process. When reading through the ZAFF paper, I saw that it was validated with ff99SB and TIP3P, while the ZAFF tutorial uses ff14SB and SPC/E. I typically use ff19SB with OPC. Are there any conflicts between ZAFF parameters and ff19SB/OPC? Also, if someone has any ideas of a better way to incorporate Zn parameters, let me know – I know that ZAFF was developed ~15 years ago now, so am not sure if something better has come along since then.
Thank you,
Kendall Cherry
Chemistry Ph.D. Student at UNC-Chapel Hill
Kratochvil Lab
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Received on Mon Jul 14 2025 - 16:00:02 PDT
