AMBER Archive (2002)

Subject: correlated motions in a protein!

From: Pradipta Bandyopadhyay (pradipta_at_cgl.ucsf.edu)
Date: Wed Feb 27 2002 - 17:52:55 CST

 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?

 Thanks.

              Pradipta

 Dr. Pradipta Bandyopadhyay
 Dept. of Pharmaceutical Chemistry
 University of California, San Francisco (UCSF)