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

[Tsjerk Wassenaar]

Hi JIom,

There is no check for correspondence of atoms. Honestly, you don't want to
have programs trying do that kind of thinking for you unthinkingly. You
should make sure that the atom order in the reference structure corresponds
to the other structure. Your RMSD may seem reasonable though, because there
are spatial correlations between the atoms which are swapped.

Cheers,

Tsjerk

On Wed, Sep 17, 2014 at 3:24 PM, gromacs query <gromacsquery at gmail.com>
wrote:

> 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
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-- 
Tsjerk A. Wassenaar, Ph.D.