[gmx-users] How to obtain a approperiate PDB file of DNA?

Mark Abraham Mark.Abraham at anu.edu.au
Fri Apr 10 05:45:36 CEST 2009

li ming wrote:
> Hi, all...
> I have a question on the pdb files of DNA:
> How can I obtain an appropriate DNA pdb file for GMX simulation? I just 
> download some pdb files from Internet, but it is not compatible for GMX, 
> saying that the residue was not found in rtp file. How can I solve this 
> problem? Are the references available on this problem?

Perhaps you should start by searching for some tutorial material with 
emphasis on these types of simulation.

> Furthermore, if I want to get several DNA pdb files 
> with increasing degree of polymerization (such as 10, 20, 50 etc.). How 
> can I achieve this goal? 

This may or may not be easy to achieve, but you should start by 
describing it more fully. What are you wanting to polymerize, and what 
do you mean by that word?


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