AMBER Archive (2003)

Subject: RE: AMBER: Radius of Gyration and RMSD

From: Endres, Robert G. (endresrg_at_ornl.gov)
Date: Tue Oct 28 2003 - 08:36:27 CST

Dear Jagannadh,
both ptraj and carnal can calculate RMSD w.r.t. a reference structure.
I still cannot figure out how to calculate the radius of gyration (had the same question a few days ago).

Robert

-----Original Message-----
From: owner-amber_at_scripps.edu on behalf of Jagannadh B
Sent: Tue 10/28/2003 4:36 AM
To: amber_at_scripps.edu
Cc:
Subject: AMBER: Radius of Gyration and RMSD
Dear AMBER- Netters

I am looking for information on comparing two structures especially of
the two methods Radius of Gyration (Moment of Inertia) and RMSD. The
information I am looking for is the criteria to confirm two structures
are indentical or not using these two methods.

Thanking you in advance

Jagannadh

*******************
Dr.B.Jagannadh
Divn of Organic Chemistry III
Indian Institute of Chemical Technology
Hyderabad 500007
INDIA
Phone: +91-40-27193155
Fax +91-40-27160512
email:jagan_at_iict.ap.nic.in
      jagan_at_iict.res.in
      bjbio_at_yahoo.com

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