Hi Xiaoming,
I would download pdb2pqr 1.8 from the apbs website and install it.
(linux)
It can handle nucleic acid, (3 letter code) .
After you installed it run it with
python /whereeveritis/pdb2pqr-1.8/pdb2pqr.py -h
it will print the options.
Hope this helps.
Fred
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