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

li ming mingli1986 at gmail.com
Fri Apr 10 05:24:04 CEST 2009

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?

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?

Thanks a lot!

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