Dear Amber community,
I’m new to the AMBER force field and would appreciate clarification on two points:
1. What is the recommended procedure for using terminal capping groups (e.g., ACE, NME) and for incorporating non-standard amino acid stereochemistry within AMBER-based workflows?
2. Is it possible to define additional capping groups beyond those provided by default? If so, can these be exported or converted for use in GROMACS? Since GROMACS supports only a limited set of caps for amber force fields, I’m wondering what the best practice is when AMBER offers capping groups that are not already available in GROMACS.
Thank you for your guidance.
Best regards
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Received on Tue Dec 02 2025 - 09:00:03 PST
