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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