Re: AMBER: Modified nucleotides-ATOM TYPES

From: David A. Case <>
Date: Mon, 26 Feb 2007 06:21:16 -0800

On Mon, Feb 26, 2007, mathew k varghese wrote:
> I am trying to parametrise a modified nucleotide. The DNA molecule which I
> am trying to simulate contains normal nucleotides as well as modified ones.
> When I am assigning AMBER atom types, there are some missing angle
> parameters. So I tried GAFF, and in this case there are no missing
> parameters. My question is, Is it a reasonable approach to use amber atom
> type and gaff atom type for the same molecule? If not how can I assign
> missing parameters for amber atom types?

Yes: what you did is reasonable. By design, it is expected that people will
use gaff and Amber parameters together.

But remember, GAFF is an automated procedure, and might not be as good as a
hand-parameterized process. You might look at this modified nucleotide force
field data base:

to see if your modification is already there, or if it gives you some ideas.

...good luck...dac

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Feb 28 2007 - 06:07:21 PST
Custom Search