AMBER Archive (2004)

Subject: Re: AMBER: RNA sequence with DNA backbone?

From: David A. Case (case_at_scripps.edu)
Date: Mon Jul 12 2004 - 15:35:43 CDT

On Mon, Jul 12, 2004, Arvind wrote:
>
> i am planning to do a MD simulation of a nucgen generated dodecamer
> CGCAAAUUUGCG but with a DNA backbone. Is this possible in AMBER?

Yes, but you will need to create a deoxy-U residue. I would recommend
starting with thymine, and using the "edit" command in LEaP to remove
the methyl group and replace it with an H. You will either have to run
RESP to get charges, or hand-merge the uracil charges into your residue.
Then you can build the molecule you want.

...good luck...dac

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