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 - 13:00:04 PDT
