AMBER Archive (2006)

Subject: Re: AMBER: nonplanarity of NH2 groups

From: FyD (fyd_at_u-picardie.fr)
Date: Thu Dec 07 2006 - 11:17:54 CST

Quoting laura zanet <laura.zanet_at_yahoo.com>:

> My question is about NH2 non-planarity. If I carry out AMBER
> minimizations on nucleic acids, what kind of non-planarities can I
> expect? For example, is it normal to get a value of 10 degrees for
> the N3-C4-N4-H41 dihedral in cytosine? I know the AMBER force feild
> cannot model this type of non-planarities, but I want to know if
> deviations from planarity of 10-15 degrees are normal.

In R.E.DD.B. you have many projects about usual/unusual DNA/RNA
fragments. In each project you obviously have the charge values for
the target whole molecules or molecule fragments provided to the
Tripos mol2 file format.
However, in a project, you also have PDB files of the whole molecules
optimized by QM (PDB file with 4 digits). Indeed, R.E.D.D.B. can also
be seen as a DB for small whole molecules optimized by QM...

You can download R.E.DD.B. projects and look at the NH2
non-planarities values for the nucleosides available in those project.
The F-60 project is a perfect example.

regards, Francois

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