AMBER Archive (2004)

Subject: Re: AMBER: Z-DNA

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Thu Jun 17 2004 - 15:00:55 CDT

> Mapped residue G, term: Terminal/beginning, seq. number: 0 to: DG5.
> Mapped residue C, term: Terminal/last, seq. number: 1 to: DC3.

The 1st residue is seen as terminal. This is good.

The 2nd residue is seen as terminal. This is not good
unless you intend a 2-residue strand. Possibly there
is a TER line after the 2nd residue? Perhaps (given
the zig-zag structure of Z-form) you have your residue
order like so, showing base pairs, with numbers referring
to order in the pdb file:

   res1 res3
   res2 res4
   ter ter
   res5 res7
   res6 res8
 ...

If so, you need to order the pdb like this:

   strand1 (5'-3')
   ter
   strand2 (5'-3')

PLUS, look at the atom name problems you are having:

> Created a new atom named: P within residue: .R<DG5 1>
> Created a new atom named: OP1 within residue: .R<DG5 1>
> Created a new atom named: OP2 within residue: .R<DG5 1>

The atoms have to be named as in the amber residue templates,
or you can use pdbAtomMap in leap to map your atom names to
the template ones.

Bill
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