Selecting and rewriting trajectory for specific atom groups

User discussions
1

hey,
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).

2

The .xtc file holds only coordinates and box information, so you don’t need to do anything with it. You could regenerate a .tpr file after modifying both your .top and coordinate files with the new residue name. Otherwise, teach whatever tool you’re using that HSD and HIS are equivalent for this purpose.

You don’t need to create a new trajectory, you just need to generate an index group that has the atom numbers you want using make_ndx. You can select by range of atoms rather than residue or chain.