AMBER Archive (2008)

Subject: AMBER: to understand how frcmod.ff99SB works

From: Alan (alanwilter_at_gmail.com)
Date: Thu Aug 28 2008 - 05:29:18 CDT

Dears,
So, I would like to understand what exactly is happening to parameters when
you load from frcmod.ff99SB.

So in tleap, loading leaprc.ff99SB, it will first load parm99.dat and then
frcmod.ff99SB. Taking a set o parameter to illustrate, we have in
parm99.dat, DIHE:

C -N -CT-C 1 0.850 180.000 -2. C -N -CT-C 1 0.800 0.000 1.

Looking at frcmod.ff99SB, we have:

C -N -CT-C 1 0.00 0.0 -4. four amplitudes
and
C -N -CT-C 1 0.42 0.0 -3. phases for phi
C -N -CT-C 1 0.27 0.0 -2.
C -N -CT-C 1 0.00 0.0 1.

So what exactly is happening here? Are those 4 new entries added to the 2
first original or the simply replacing them?

Many thanks in advance.

Cheers,
Alan 

-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<

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