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
Received on Fri Jan 17 2003 - 17:12:35 PST
