AMBER Archive (2006)

Subject: Re: AMBER: Ringof dna

From: f m (
Date: Thu Jul 13 2006 - 12:00:48 CDT

Thankyou, I'll try that!


>From: "David A. Case" <>
>Subject: Re: AMBER: Ringof dna
>Date: Thu, 13 Jul 2006 09:54:07 -0700
>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
> > 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
>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
>Don't forget to use the "bond" command to add the bond between the first
>last residues of the circle.
>...good luck...dac
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