Re: missing parameters

From: Jie Lu <>
Date: Wed 25 Oct 2000 19:38:31 -0400 (EDT)

I have read the 'develop new parameter' section and fully understand how
to do it for the example CH3-CH3 and CH2=CH2. But in my case, the missing
parameter in the five-member ring.(N*-CA). When I try to develop the
dihedral parameter, such as C-N8-CA-N2, there are 2 questions.
First, the angle can varied only in a small range.
second, the geometry of other part of this structure could also be
influenced by this parameter.
So is it the right way to develop this parameter: choose possible range
of that dihedral, fix the dihedral and minimize the structure with
gaussin as well as AMBER to get the energy?

               O6 R R
               || \ /
       N7 C6(C) C14(CT)
     // \ / \ / \ //
           C5 N1(N*)_____C15(CT) C13(CA)
H8--C8 || | | |
           C4 C2(CA) C10(CT) C12(CA)
     \ / \ // \ / | \ / \\
       N9 N3 N2(N2) R C11(C)
       | | ||
       H2 H21 O9(O)

Your help is highly appreciated
Jie Lu

 On Fri, 20 Oct 2000, Bill
Ross wrote:

> I should develop my own parameter using analogy. Is it right?
> It's a possibility, otherwise search the literature in case
> someone else has done it, or follow the references in that
> section to papers on how to do it numerically.
> Bill Ross
Received on Wed Oct 25 2000 - 16:38:31 PDT
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