On Tue, Apr 23, 2024, Eric Pettersen via ChimeraX-users wrote:
I wouldn't call having the 5' end of a nucleic acid chain phosphorylated a problem. Some entries have that (e.g. 6zz6) and some don't (e.g. 1bna). Amber doesn't support 5' phosphorylation simulation, so as you found you need to delete it yourself.
FWIW: Amber *does* support 5' phosphorylation, but it is admittedly not well-described in the documentation (should change soon.) You need to load the "terminal_monophosphate.lib" file after loading the standard DNA or RNA leaprc files. [Things are more complicated if you need to control the protonation states, or if some chains have a 5' phosphate and others do no, etc.] Don't hesitate to ask questions at the Amber mailing list.] ...dave case