[gmx-users] rmsd of the same protein

[Anton Feenstra]

QZ wrote:

> 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.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
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|  _   _  ___,| K. Anton Feenstra                                     |
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