feenstra at few.vu.nl
Mon Jan 3 18:17:46 CET 2005
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.
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