VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
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.
http://www.rcsb.org/pdb/101/motm_disscussed_entry.do?id=1bna

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

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.

Best,
/A

On Sat, Jul 4, 2015 at 5:01 AM, Mohsen Farshad <mohsen.farshad_at_maine.edu>
wrote:

> 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.
> 

-- 
Best,
/A