AMBER Archive (2004)

Subject: AMBER: Z-DNA

From: xiaowei li (xl3a_at_virginia.edu)
Date: Thu Jun 17 2004 - 13:43:13 CDT

Dear amber users:
   When I tried to load the PDB file of Z-form DNA decamer (ID: 279d)
into LEap, I got error message which is posted below. I checked it again
and surprised to find that:
(1) There are 12 base pairs in the pdb file. I am curious to know why it
is 12 instead of 10 because the decamer has only 10 base pairs.
(2) The backbone of this decamer is broken (not all phosphate groups
connected) in the DNA when I took a close look at the structure by xleap.
Thanks for your help.

(error message)
Loading PDB file: ./279d.pdb1
Matching PDB residue names to LEaP variables.
Mapped residue G, term: Terminal/beginning, seq. number: 0 to: DG5.
Mapped residue C, term: Terminal/last, seq. number: 1 to: DC3.
Mapped residue G, term: Terminal/beginning, seq. number: 2 to: DG5.
Mapped residue C, term: Terminal/last, seq. number: 3 to: DC3.
Mapped residue G, term: Terminal/beginning, seq. number: 4 to: DG5.
Mapped residue C, term: Terminal/last, seq. number: 5 to: DC3.
Mapped residue G, term: Terminal/beginning, seq. number: 6 to: DG5.
Mapped residue C, term: Terminal/last, seq. number: 7 to: DC3.
Mapped residue G, term: Terminal/beginning, seq. number: 8 to: DG5.
Mapped residue C, term: Terminal/last, seq. number: 9 to: DC3.
Mapped residue G, term: Terminal/beginning, seq. number: 10 to: DG5.
Mapped residue C, term: Terminal/last, seq. number: 11 to: DC3.
Mapped residue G, term: Terminal/beginning, seq. number: 12 to: DG5.
Mapped residue C, term: Terminal/last, seq. number: 13 to: DC3.
Mapped residue G, term: Terminal/beginning, seq. number: 14 to: DG5.
Mapped residue C, term: Terminal/last, seq. number: 15 to: DC3.
Mapped residue G, term: Terminal/beginning, seq. number: 16 to: DG5.
Mapped residue C, term: Terminal/last, seq. number: 17 to: DC3.
Mapped residue G, term: Terminal/beginning, seq. number: 18 to: DG5.
Mapped residue C, term: Terminal/last, seq. number: 19 to: DC3.
Mapped residue G, term: Terminal/beginning, seq. number: 20 to: DG5.
Mapped residue C, term: Terminal/last, seq. number: 21 to: DC3.
Mapped residue G, term: Terminal/beginning, seq. number: 22 to: DG5.
Mapped residue C, term: Terminal/last, seq. number: 23 to: DC3.
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>
Joining DG5 - DC3
Created a new atom named: OP1 within residue: .R<DC3 2>
Created a new atom named: OP2 within residue: .R<DC3 2>
   Added missing heavy atom: .R<DC3 2>.A<O1P 2>
   Added missing heavy atom: .R<DC3 2>.A<O2P 3>
Created a new atom named: P within residue: .R<DG5 3>
Created a new atom named: OP1 within residue: .R<DG5 3>
Created a new atom named: OP2 within residue: .R<DG5 3>
Joining DG5 - DC3
Created a new atom named: OP1 within residue: .R<DC3 4>
Created a new atom named: OP2 within residue: .R<DC3 4>
   Added missing heavy atom: .R<DC3 4>.A<O1P 2>
   Added missing heavy atom: .R<DC3 4>.A<O2P 3>
Created a new atom named: P within residue: .R<DG5 5>
Created a new atom named: OP1 within residue: .R<DG5 5>
Created a new atom named: OP2 within residue: .R<DG5 5>
Joining DG5 - DC3
Created a new atom named: OP1 within residue: .R<DC3 6>
Created a new atom named: OP2 within residue: .R<DC3 6>
   Added missing heavy atom: .R<DC3 6>.A<O1P 2>
   Added missing heavy atom: .R<DC3 6>.A<O2P 3>
Created a new atom named: P within residue: .R<DG5 7>
Created a new atom named: OP1 within residue: .R<DG5 7>
Created a new atom named: OP2 within residue: .R<DG5 7>
Joining DG5 - DC3
Created a new atom named: OP1 within residue: .R<DC3 8>
Created a new atom named: OP2 within residue: .R<DC3 8>
   Added missing heavy atom: .R<DC3 8>.A<O1P 2>
   Added missing heavy atom: .R<DC3 8>.A<O2P 3>
Created a new atom named: P within residue: .R<DG5 9>
Created a new atom named: OP1 within residue: .R<DG5 9>
Created a new atom named: OP2 within residue: .R<DG5 9>
Joining DG5 - DC3
Created a new atom named: OP1 within residue: .R<DC3 10>
Created a new atom named: OP2 within residue: .R<DC3 10>
   Added missing heavy atom: .R<DC3 10>.A<O1P 2>
   Added missing heavy atom: .R<DC3 10>.A<O2P 3>
Created a new atom named: P within residue: .R<DG5 11>
Created a new atom named: OP1 within residue: .R<DG5 11>
Created a new atom named: OP2 within residue: .R<DG5 11>
Joining DG5 - DC3
Created a new atom named: OP1 within residue: .R<DC3 12>
Created a new atom named: OP2 within residue: .R<DC3 12>
   Added missing heavy atom: .R<DC3 12>.A<O1P 2>
   Added missing heavy atom: .R<DC3 12>.A<O2P 3>
Created a new atom named: P within residue: .R<DG5 13>
Created a new atom named: OP1 within residue: .R<DG5 13>
Created a new atom named: OP2 within residue: .R<DG5 13>
Joining DG5 - DC3
Created a new atom named: OP1 within residue: .R<DC3 14>
Created a new atom named: OP2 within residue: .R<DC3 14>
   Added missing heavy atom: .R<DC3 14>.A<O1P 2>
   Added missing heavy atom: .R<DC3 14>.A<O2P 3>
Created a new atom named: P within residue: .R<DG5 15>
Created a new atom named: OP1 within residue: .R<DG5 15>
Created a new atom named: OP2 within residue: .R<DG5 15>
Joining DG5 - DC3
Created a new atom named: OP1 within residue: .R<DC3 16>
Created a new atom named: OP2 within residue: .R<DC3 16>
   Added missing heavy atom: .R<DC3 16>.A<O1P 2>
   Added missing heavy atom: .R<DC3 16>.A<O2P 3>
Created a new atom named: P within residue: .R<DG5 17>
Created a new atom named: OP1 within residue: .R<DG5 17>
Created a new atom named: OP2 within residue: .R<DG5 17>
Joining DG5 - DC3
Created a new atom named: OP1 within residue: .R<DC3 18>
Created a new atom named: OP2 within residue: .R<DC3 18>
   Added missing heavy atom: .R<DC3 18>.A<O1P 2>
   Added missing heavy atom: .R<DC3 18>.A<O2P 3>
Created a new atom named: P within residue: .R<DG5 19>
Created a new atom named: OP1 within residue: .R<DG5 19>
Created a new atom named: OP2 within residue: .R<DG5 19>
Joining DG5 - DC3
Created a new atom named: OP1 within residue: .R<DC3 20>
Created a new atom named: OP2 within residue: .R<DC3 20>
   Added missing heavy atom: .R<DC3 20>.A<O1P 2>
   Added missing heavy atom: .R<DC3 20>.A<O2P 3>
Created a new atom named: P within residue: .R<DG5 21>
Created a new atom named: OP1 within residue: .R<DG5 21>
Created a new atom named: OP2 within residue: .R<DG5 21>
Joining DG5 - DC3
Created a new atom named: OP1 within residue: .R<DC3 22>
Created a new atom named: OP2 within residue: .R<DC3 22>
   Added missing heavy atom: .R<DC3 22>.A<O1P 2>
   Added missing heavy atom: .R<DC3 22>.A<O2P 3>
Created a new atom named: P within residue: .R<DG5 23>
Created a new atom named: OP1 within residue: .R<DG5 23>
Created a new atom named: OP2 within residue: .R<DG5 23>
Joining DG5 - DC3
Created a new atom named: OP1 within residue: .R<DC3 24>
Created a new atom named: OP2 within residue: .R<DC3 24>
   Added missing heavy atom: .R<DC3 24>.A<O1P 2>
   Added missing heavy atom: .R<DC3 24>.A<O2P 3>
   total atoms in file: 492
   Leap added 312 missing atoms according to residue templates:
        24 Heavy
        288 H / lone pairs
   The file contained 60 atoms not in residue templates 

-- 
Xiaowei Li
Department of Electrical and Computer Engineering
University of Virginia
924-3446(O)

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