Hi Kendall,
You are not alone. Please see this AMBER email list too
http://archive.ambermd.org/202405/0040.html (Apology to Saverio that I did not notice it until today).
This is a good chance to bring them together and resolve the issue. I believe some rare instances were being missed by the Seminario/ChgModB method during parameter generation. Please allow me a couple of days to look into it and get back to you by the end of August. Appreciate your patience.
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 <kche.email.unc.edu>
Sent: Monday, July 14, 2025 7:57 PM
To: Li, Zhen <lizhen6.chemistry.msu.edu>; amber.ambermd.org <amber.ambermd.org>
Subject: Re: [AMBER] Choice of protein/water force fields with ZAFF zinc parameters?
Hi Zhen,
Thank you for the clarification. I encountered an error message today that I believe is a problem with the ZAFF.frcmod file. In tleap, when I tried to save the .prmtop and .inpcrd files (after loading ZAFF.frcmod and ZAFF.prep), I got numerous errors that the bond, angle, and torsion types were not found. I replaced all instances of ZN with Zn2+ in the ZAFF.frcmod file, as my ZN ions were being renamed to Zn2+, and tried again. This got rid of the angle and bond issues, but the torsion errors remain. Here is just a portion of that:
Error: ** No torsion terms for atom types: CC-N1-Zn2+-S2
for atom CG at position -5.464000, -0.251000, -1.623000,
atom ND1 at position -6.101000, 0.958000, -1.517000,
atom ZN at position -5.284000, 2.719000, -2.043000,
and atom SG at position -3.460000, 2.371000, -3.448000.
Error: ** No torsion terms for atom types: S1-Zn2+-S1-CT
for atom SG at position 5.739000, 7.577000, 1.386000,
atom ZN at position 5.749000, 7.446000, 3.664000,
atom SG at position 7.872000, 7.200000, 4.458000,
and atom CB at position 9.127000, 7.334000, 3.145000.
Error: ** No torsion terms for atom types: CT-S1-Zn2+-S1
for atom CB at position 5.446000, 5.958000, 0.614000,
atom SG at position 5.739000, 7.577000, 1.386000,
atom ZN at position 5.749000, 7.446000, 3.664000,
and atom SG at position 7.872000, 7.200000, 4.458000.
This repeated dozens of times, all of the torsion terms containing Zn2+. I checked the modified ZAFF.frcmod file and noticed that some of the torsion terms that caused errors were still present there, so I am not sure what is going wrong. Some torsion terms are missing, though, so I will need to create new ones I’m assuming?
If I can provide any other information, files, etc. for clarification, please let me know.
Thank you,
Kendall Cherry
From: Li, Zhen <lizhen6.chemistry.msu.edu>
Date: Monday, July 14, 2025 at 6:33 PM
To: amber.ambermd.org <amber.ambermd.org>, Cherry, Kendall <kche.email.unc.edu>
Subject: Re: [AMBER] Choice of protein/water force fields with ZAFF zinc parameters?
You don't often get email from lizhen6.chemistry.msu.edu. Learn why this is important<
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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<
https://urldefense.com/v3/__http://lizhen62017.wixsite.com/home__;!!HXCxUKc!3p1mfOlkidzTUaa3S0PkMcNd0BhmqN4kybdqj5cSljXXxvi-g2WQJ3sSRlqaQq0hw8B_OmZUSPV3PJbudXVYFMc0$>, Ph.D.,
The Merz Research Group<
https://urldefense.com/v3/__http://merzgroup.org/__;!!HXCxUKc!3p1mfOlkidzTUaa3S0PkMcNd0BhmqN4kybdqj5cSljXXxvi-g2WQJ3sSRlqaQq0hw8B_OmZUSPV3PJbuddSBpDyQ$>,
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 Tue Jul 15 2025 - 03:00:02 PDT
