AMBER Archive (2009)

Subject: [AMBER] Single Adenine

From: ros (ros_at_servidor.unam.mx)
Date: Wed Aug 26 2009 - 01:09:23 CDT

Hello to all!
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.

Is there a template for single purine or pirimidine molecules?

Thanks for the help!

ros

Instituto de Quimica
Universidad Nacional Autónoma de México
unam.mx
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