RMSD Question

From: snoze pa (snoze.pa_at_gmail.com)
Date: Sun Nov 28 2010 - 11:08:25 CST

Dear NAMD/VMD Users,

 I am trying to calculate the RMSD between two proteins. One has
crystal structure and other is a model structure. I used modeller to
model the protein. When I calculate rmsd between model structure and
crystal structure then rmsd is fine, close to the rsolution of the
crystal structure. But When I minimize the structure using namd then
the rmsd increses up to 1.4 A.

So do you think I should also minimize the crystal structure also to
calculate the correct rmsd. Becuase in the minimzed model structure
the loop regions changes sometime, which may be true if we will
minimize the crystal structure.

Which is the correct way to calculate the RMSD? Please guide me.

Thank you for your help in advance.


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