AMBER Archive (2006)

Subject: Re: AMBER: Ringof dna

From: David A. Case (case_at_scripps.edu)
Date: Thu Jul 13 2006 - 11:54:07 CDT

On Thu, Jul 13, 2006, Flora Mactavish wrote:

> I am attempting to use amber to analyse a ring of dna.
>
> Is there a command to tell Amber that it is dealing with a ring, or any way
> around this problem?

You have to modify the leaprc file to do this. Make a copy of whatever you
are using (probalby leaprc.ff94 or leaprc.ff99) , and look at the addPdbResMap
section. At the bottom of this section are commands that make the default
first residue a "5" and the default final residue a "3"-type residue. You
don't want that for a circle -- you could actually remove the entire
addPdbResMap section for your copy, and load that instead of the default one.

Don't forget to use the "bond" command to add the bond between the first and
last residues of the circle.

...good luck...dac

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