[gmx-users] sequence of atoms different for rmsd reference structure

[gromacs query]

Hi All

I have one PDB structure which I want to use as reference for rmsd
calculation (with best fitting). But I realize in my gromacs trajectory the
same structure (if written in PDB) has different sequence of atoms and some
different atom names (especially H, OP1 vs O1P and O2P vs OP2) compared to
reference.

e.g. comparing say first few atoms in structure to be compared has this
sequence

ATOM      1  O5'  DG     1      88.750  97.070 107.880  1.00
0.00
ATOM      2  H5T  DG     1      89.730  97.100 108.050  1.00
0.00
ATOM      3  C5'  DG     1      88.150  98.370 108.180  1.00  0.00
ATOM      4 1H5'  DG     1      88.610  99.040 107.590  1.00
0.00
ATOM      5 2H5'  DG     1      88.360  98.560 109.130  1.00  0.00


and the reference structure has this:

ATOM      1 HO5' DG5     1      12.843 -51.888  -5.899  1.00
0.00           H
ATOM      2  O5' DG5     1      13.094 -52.038  -5.621  1.00
0.00           O
ATOM      3  C5' DG5     1      13.037 -51.978  -4.813  1.00
0.00           C
ATOM      4  H5' DG5     1      13.096 -51.378  -4.805  1.00
0.00           H
ATOM      5 H5'' DG5     1      13.617 -52.139  -4.669  1.00
0.00           H


The RMSD plots am getting are quite expected and gromacs does not complain
about atom names. Is it due to best fitting method that should take care of
this (I am not using mass-weighted RMSD, so simply it is non-mass weighted
best fitted with rotation+translation)

or do I need to keep same sequence and atom names in my reference structure
as in my Gromacs structure/traj for RMSD calc.?

Thanks for any help
JIom