AMBER Archive (2009)

Subject: Re: [AMBER] Single Adenine

From: case (case_at_biomaps.rutgers.edu)
Date: Wed Aug 26 2009 - 06:36:09 CDT

On Wed, Aug 26, 2009, ros wrote:

> I am trying to study the interaction of a Cu(II) compund with adenine. I
> have working prmtop and inpcrd for the metal-compound but cant get a single
> adenine molecule to work. I tried using the residues from the force fields
> (DA, DA3, DA5, etc) but these are the full nucleotide. So I tried drawing
> one by hand and relaxing the structure using g03, exporting to PDB and using
> antechamber to generate the frcmod file. When I fire up xleap and load the
> adenine.pdb, it gets recognized as DA3 and displays broken bonds and missing
> atoms.

First, the pdb file would only be "recognized as DA3" if its name is DA3. So,
you might just need to change the residue name in the pdb file. Second, DAN
(the deoxy adenine nucleoside) is probably closest to what you want.

...good luck...dac

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