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

li ming mingli1986 at gmail.com
Fri Apr 10 06:21:33 CEST 2009

Hi, Mark:

I want to check the chain length of DNA on the translocation time through a
nanopore. So the DNA chains with different polymerization but the same
monomer structure is necessary. How can I solve this problem?

Does anybody has a optimized DNA pdb file for GMX simulation?

Thanks a lot!!


2009/4/10 Mark Abraham <Mark.Abraham at anu.edu.au>

> 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?
> Mark
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Ming Li
Institute of Chemistry,Chinese Academy of Sciences
Zhongguancun, Beijing, 100080, P. R. China
Tel: +86-10-13811601014 / 62564829
E-mail: liming at iccas.ac.cn / mingli1986 at gmail.com
Knowledge is a city to the building of which every human being brought a
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