AMBER Archive (2006)

Subject: AMBER: force field parameters

From: Douali, Latifa (latifa.douali_at_pnl.gov)
Date: Thu May 18 2006 - 12:33:35 CDT

Dear AMBER users,

I am running an MD simulation for a non standard nucleic acid which is
non planar.
In this structure, I have a methyl group in a pseudo axial position.
My question is:
1) how can I prevent this methyl from inverting to the equatorial
position.
The improper dihedrals I used for these simulations are as follow:

CT-C-N*-CT 1.1 180.0 2.0
CT-C-N*-CM 1.1 180.0 2.0
C-CT-CT-CT 1.1 180.0 2.0
N*-OH-CT-HC 1.1 180.0 2.0
CT-OH-CT-HC 1.1 180.0 2.0
N*-CT-CT-HC 1.1 180.0 2.0

2) May the proper dihedral angles also play a role in this transition
Attached is the structure of this system with the atom types assigned. I
might be doing something wrong,
any advice will be welcome

Latifa


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