Hello All,
I’m trying to use Avogadro’s peptide building capabilities to build a peptide system to be used with CHARMM19. CHARMM19 is a united atom model but still has polar hydrogens (hydrogens attached to N and O). Avogadro will allow me to remove “all” hydrogens, this inherently removes polar hydrogens. Is it possible to remove all hydrogens except polar, while also keeping the atoms correctly labeled, as in CA for alpha carbon?
Thanks,
John