> 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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Thu Jun 17 2004 - 21:53:01 PDT
