AMBER Archive (2006)

Subject: AMBER: RMSD: is it related to flexibility?

From: a a (
Date: Wed Oct 04 2006 - 04:42:12 CDT

Dear All,

I got two protein structures with different performance on the loop
mobilitiy, one of them move very fast, another one is about 10 time less
flexible, based on our experimental data.

I could like to ask if it is sensible to do molecular dyanmics calculations
if I could like to get an explaination for these differences, how can I
determine the flexibility of a structure? Did the RMSD analysis could tell
the flexiblity of two loop?

Best regards,


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