AMBER Archive (2006)

Subject: RE: AMBER: force field parameters

From: Douali, Latifa (latifa.douali_at_pnl.gov)
Date: Thu May 18 2006 - 13:40:53 CDT

 Thank you for reply. But in my understanding is that CM is an sp2
carbon

Latifa

Hello Douali;

I think the problem is with defining CM, because in png file I can see
the methyl carbon as CT . You can change your atom type as CM.

It will work.

Good luck,

Navnit

Douali, Latifa wrote:

>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
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