AMBER Archive (2004)

Subject: AMBER: question about nmode

From: xiaowei li (xl3a_at_virginia.edu)
Date: Tue Oct 05 2004 - 13:09:15 CDT

Dear amber users:
    I am trying to obtain the normal modes of DNA with 12 base pairs. I
think seven control flags, i.e. CUT, SCNB, SCEE,DIELC, IDIEL, IPOL and
I3BOD are crucial for the result. I have performed normal modes
calculation of one DNA molecule using the default values for all these
seven flags. There is obvious difference between the calculated
eigenfrequencies with NMODE and resonace frequencies in meausred
absorption spectra. So I am wondering whether different assignments of
these seven flags will change the calcualted eigenfrequencies
dramtically. Additionally, I would like to know physical meaning of
SCNB and SCEE. Thank you.
Best, 

-- 
Xiaowei Li
Department of Electrical and Computer Engineering
University of Virginia
924-3446(O)

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