AMBER Archive (2004)

Subject: Re: AMBER: question about nmode

From: David A. Case (case_at_scripps.edu)
Date: Tue Oct 05 2004 - 14:03:52 CDT

On Tue, Oct 05, 2004, xiaowei li wrote:

> 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.

You certainly want to set CUT to a very large value. It's not clear with
the current codes how to mimic the solvent + ion distribution (Gen Born is
not yet set up for normal modes). You could try setting IDIEL=0 (for
distance-dependent dielectric) and perhaps DIELC=4. But I would not expect
great physical realism from such models.

....dac

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