Subject: N-H Correlation function in CHARMM

From: Troy Wymore <[email-masked]>
Date: Wed, 19 Nov 1997 14:36:42 -0600 (CST)

I would like to construct a correlation function for N-H vectors in my
peptide from trajectory files using CHARMM version 24b2.  People have done
this to make the connection between the motion of the peptide and NMR
relaxation.  I know CHARMM has the NMR analysis facility which I have used
successfully; my problem is using CORREL to construct the correlation
function.

My question is this:  Do I have to rewrite the coordinate trajectory files
so that the peptide is oriented with respect to some reference structure
or can I just put in something like :
trajectory firstu 50 nunit 1 begin  779750   stop  809500   skip 250 -
orient         select type CA end (just an example)

If anyone can supply an example script where they did a similar sort of
analysis; especially for N-H vectors in proteins/peptides, it would be
appreciated.  I figured that my script should be close to the one
described in the docs for fluorescence depolarization, but something is
still wrong.

Any help would be much appreciated.

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Troy Wymore
Department of Chemistry
University of Missouri-Columbia
Columbia, MO 65211

e-mail: [email-masked]

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