[gmx-users] g_rms

[Itamar Kass]

Thank for you quick replay, when I did my small test – I used only the c-alpha,
hence the atom number shouldn’t matter (if I correct).

Quoting Anton Feenstra <feenstra at few.vu.nl>:

> Itamar Kass wrote:
>
> >   Happy new year all, I have a question which might sound strange.  While
> > calculating RMSD (using g_rms) I got strange results.  In order to check it
> I
> > calculated the rmsd between two identical structures (I just copy a
> structure).
> >  The calculated rmsd was more then a 1.5nm.  The differance between the two
> > structures was only in the absence of hydrogen in the second structure.
> > I used:
> > g_rms -s M2TMP_tet_Kim.pdb -f M2TMP_tet_Kim_2.pdb
> >
> > Does someone know what is happening here?
>
> Aside from your mail arriving four times? ;-)
>
> g_rms compares by atom numbers. If one structure includes H's, atom numbers
> will not match, resulting in arbitrarily high rmsd's. Try g_confrms and
> select equivalent groups for both structures (e.g. C-alpha, or backbone).
> For your abovementioned test, convert the one pdb file with editconf to
> exclude the H's.
>
> --
> Groetjes,
>
> Anton
>
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===========================================
| Itamar Kass
| The Alexander Silberman
| Institute of Life Sciences
| Department of Biological Chemistry
| The Hebrew University, Givat-Ram
| Jerusalem, 91904, Israel
| Tel: +972-(0)2-6585146
| Fax: +972-(0)2-6584329
| Email: ikass at cc.huji.ac.il
| Homepage: http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html
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