Dear all:
I'm having a problem create the electrostatic surface for a DNA chain
containing several modified nucleotides. APBS could not identify those residues
and reported them as unassigned.
What should I do to solve this problem?
Thanks a lot and best,
Xiaoming
Hi,
It's pdb2pqr problem (unknown residue). I guess you ran pdb2pqr prior to
running APBS, if not, you should. So, you should submit your question to either
the APBS or pdb2pqr BB's. They are very helpful people.
Cheers,
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
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
