Dear AMBER Developers,
I hope this email finds you well.
I am planning to perform constant-pH molecular dynamics simulations (CPHMD) using AMBER 2022 to study DNA behavior in solution. However, I have questions regarding the residue naming conventions for DNA protonation states at different pH conditions.
From the documentation, I understand that certain residues require name changes to reflect protonation states (e.g., ASP → AS4 at pH 7). Could you clarify how DNA bases should be renamed in such simulations? Specifically:
1. For adenine and Cytosine (currently "DA" and "DC" in standard residues), what should its nomenclature be at pH 7?
2. Are there standardized naming rules for other DNA bases (e.g., cytosine, guanine, thymine) under constant-pH conditions?
If CPHMD for DNA isn't fully implemented, are there recommended workarounds (e.g., manual protonation state adjustments)?
I would greatly appreciate any guidance or references to relevant documentation. Thank you for your time and support!
Best regards,
Shiyu Wang
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Received on Wed Apr 09 2025 - 21:00:02 PDT
