From: Ashar Malik (
Date: Fri Jul 03 2015 - 13:18:23 CDT

Normally, DNA strands are created using visualizers. They give options to
create single or double stranded DNA, in 1 of its 3 states. e.g.

As far as the topology file is concerned - they are covered in the *_na.*

Also DNA is just a combination of the 4 basic nucleotides -- you don't need
a specific topology for a stretch of DNA. The same file works for all
possible sequences - just like the protein one.


On Sat, Jul 4, 2015 at 5:01 AM, Mohsen Farshad <>

> Hi,
> I am going to simulate ssDNA, how can I find related pdb and topology
> files for a specific DNA, please give me some tutorials as examples to do.
> Best,
> Mohsen Farshad.