[gmx-users] g_rms

[Anton Feenstra]

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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|  _   _  ___,| K. Anton Feenstra                                     |
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