correlated motions in a protein!

From: Pradipta Bandyopadhyay <>
Date: Wed 27 Feb 2002 15:52:55 -0800 (PST)

 I want to see if there is any correlation among the motions of different
parts of a protein.

 I am thinking of doing the following things:

 (1) Visualize the low frequency modes (both cartesian and internal).

 (2) RMSD for each residue for one MD trajectory.

 (3) Time correlation function of internal coordinates.

 I can use Nmanal for (1) - does any body have a sample input file for
 this and some experience in using it?

  Nmanal manual says it is possible to calculate (3) also with it - has
 anyone done it?

 And finally what are the other quantitites I can look for to get the
 'correlated motions'? Can AMBER do these?



 Dr. Pradipta Bandyopadhyay
 Dept. of Pharmaceutical Chemistry
 University of California, San Francisco (UCSF)
Received on Wed Feb 27 2002 - 15:52:55 PST
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