[AMBER] Structural alignment & RMSD calculation

From: Rahul Banerjee <rahul.banerjee.chemistry.msu.edu>
Date: Mon, 7 Feb 2011 13:50:14 -0500

Dear All,

How can I calculate RMSD for a given region in the protein by aligning the core structure with a given crystal structure? I have made some changes in the protein (mutation) and due to that some loop regions are likely to become flexible. Where the core structure is unlikely to move. I have crystal structure of the mutated form as well, that I can use as reference in the alignment process.

Thanking you.

With best regards,

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Received on Mon Feb 07 2011 - 11:00:07 PST
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