Re: RNA to DNA

From: Leonardo Trabuco (
Date: Mon Jul 10 2006 - 10:51:21 CDT


On Sat, Jul 08, 2006 at 10:59:24AM +0530, wrote:
> I am trying to prepare the psf file for a multichain protein-dna complex
> and I am using the top_all27_prot_na.inp topology file.
> I am not sure whether I have understood this correctly-
> From what I see in the topology file, the residues ADE, GUA, THY, CYT are
> for RNA and not DNA. And so since I am using DNA, I would need to use the
> DEO1, and DEO2 patches to convert the RNA to DNA for pyrimidines and
> purines respt.
> And I am trying to do the conversion using the atomselect feature in VMD
> to determine which of the nucleic acid residues are pyrimidine and which
> are purine, and use the corresponding patch for each of 350 DNA atoms that
> I have.
> However, I am running into difficulties.
> So I would like to check - am I on the right track? And how would you
> suggest that I do the conversion?

That's exactly what you have to do. What difficulties are you running


Leonardo Giantini Trabuco
Ph.D. candidate
Center for Biophysics and Computational Biology
University of Illinois at Urbana-Champaign

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