AMBER Archive (2003)

Subject: nucleic acid structures

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Fri Jan 17 2003 - 19:12:35 CST

Hi ambers,

I am trying to read into Leap a nucleic acid structure terminated with a
phosphate. However leap complains about the terminal atoms

FATAL: Atom .R<DA5 1>.A<P 31> does not have a type.
FATAL: Atom .R<DA51>.A<OP 32> does not have a type.
FATAL: Atom .R<DA5 1>.A<O1P 33> does not have a type.
FATAL: Atom .R<DA5 1>.A<O2P 34> does not have a type.
FATAL: Atom .R<DA3 9>.A<HO3' 34> does not have a type.

I did try to edit the table in xleap and correct for the atom types, I
assume that the P atom corresponds to the regular P ff type while the O1P
and O2P to the O2 atom type.
I assume that OP should also have O2 atom type, is this correct?
The charge on this atom will also be the regular charge for O2 type of
atoms, -0.776100 ?

I am not sure though what atom type I should assign to the HO3' atom?
The regular HO ff type is good enough?

Any advice on the above matter would be of great help.

Thank you in advance,
Ioana