Le 02/12/2025 à 17:41, Xenidis, Vasilis via AMBER a écrit :
> 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?
Dear Vasilis,
I'm not sure capping (or not) has a definitive answer, so by default I'd
use what Chimera / pdb4amber would use by default,
I better trust their developpers.
For non standard amino acids, if they are not too complex (i.e. only
using modified amino acids), there a database to find some of them:
-
http://amber.manchester.ac.uk/ (for AMBER)
-
http://vienna-ptm.univie.ac.at (GROMACS and AMBER)
- MRP.py to model non existing ones (MRP.py: A Parametrizer of
Post-Translationally Modified Residues,
https://pubs.acs.org/doi/full/10.1021/acs.jcim.0c00472), that I found
useful in a recent work on modelling TPM nucleosome modifications.
(not answering the second part).
HTH,
Stéphane
--
Maître de conférences Hors Classe, PEDR, HDR
US2B, Nantes Université, CNRS, UMR 6286, Team Structural Bioinformatics, F-44000 Nantes
http://www.us2b.univ-nantes.fr/ - http://www.steletch.org
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Received on Tue Dec 02 2025 - 10:00:02 PST
