i am here with two basic questions:
I want to perform some analysis on monomers of pentameric protein. I have prepared my system using charmm gui so, there is HSD residue in my protein but when i am performing hydrophobicity related analysis on it, i am getting error for the particular residue : like there is no hydrophobicity entry for HSD. is it possible to rename HSD residue to HIS in .XTC and .tpr files?
my second query is i have to select monomer and lets say run g_rmsf on it. how can i rewrite a trajectory with specific atom residues (monomer only) here? (Charmm gui didnt gave it chain identifiers( A B C D) so cant select using that).