From: nisha_at_ncbs.res.in
Date: Sat Jul 08 2006 - 00:29:24 CDT

Hello NAMD Users

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?

As you must have realised I am new to molecular dynamics and would
appreciate your help.

With thanks and regards

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