[gmx-users] rmsd of the same protein
feenstra at chem.vu.nl
Fri Apr 23 09:08:07 CEST 2004
> Dear All,
> I have done an 8ns MD on a protein. MD was stable and equlibrated. I
> took frames between 2ns and 8ns and run g_clusters to an average
> structure. I also minimized the average structure. Now I compare this MD
> structure with its crystal structre. The RMSD is 1.5 Angstrom for the
> backbone. The big RMSD's are at loops and termini. Are these two
> structure considered the same?
No they are different at around 1.5 angstroms. Whether you would consider
that a significant difference, is quite another matter.
You might take the X-ray resolution as a measure, but some parts of the
X-ray structure will be better defined than others.
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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