AMBER Archive (2005)

Subject: AMBER: phosphorylated DNA not recognized

From: Annette Höglund (hoeglund_at_informatik.uni-tuebingen.de)
Date: Thu Mar 03 2005 - 08:55:18 CST

Dear All,

I am looking at a protein-DNA comlex, in which one DNA base (DA5 a
terminal one) is phosphorylated.
Leap does not recognize the "additional" O, O1P, O2P, and O3P attached
to the DA5.

There is a error message in leap (when converting pdb to crd and top files):
FATAL: Atom .R<DA5 6>.A<O1P 31> does not have a type.
etc.

How can I fix this in my leap script, I guess I need to add atoms to my
unit Da5 or create a complete new unit - is that correct?
Has someone already solved this?
Some help on the way would be highly appreciated!

Thanks and have a wonderful day!

/Annette

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