AMBER Archive (2006)

Subject: AMBER: NAD ??

From: Urszula Uciechowska (urszula.uciechowska_at_pharmazie.uni-halle.de)
Date: Wed Nov 08 2006 - 07:40:15 CST

Dear Amber Users,

I am trying to prepare a pdb with NAD to the xleap, but all the time I am getting such a
comments in xleap window and I have no idea how can I correct it? I tried many things but
always
I am getting the same..

This is what i got on the xleap window after loading pdb file

  ATOM NAMES IN EACH RESIDUE MUST BE UNIQUE:
     (same-name atoms are reduced to a single atom)

Unknown residue: DP number: 314 type: Terminal/last
..relaxing end constraints to try for a dbase match
  -no luck
  Added missing heavy atom: .R<LYS 56>.A<CD 11>
  Added missing heavy atom: .R<LYS 56>.A<CE 14>
  Added missing heavy atom: .R<LYS 56>.A<NZ 17>
  Added missing heavy atom: .R<LYS 197>.A<CD 11>
  Added missing heavy atom: .R<LYS 197>.A<CE 14>
  Added missing heavy atom: .R<LYS 197>.A<NZ 17>
  Added missing heavy atom: .R<LYS 289>.A<CE 14>
  Added missing heavy atom: .R<LYS 289>.A<NZ 17>
  Added missing heavy atom: .R<LYS 296>.A<NZ 17>
  Added missing heavy atom: .R<LYS 306>.A<NZ 17>
  Added missing heavy atom: .R<LYS 317>.A<CE 14>
  Added missing heavy atom: .R<LYS 317>.A<NZ 17>
  Added missing heavy atom: .R<CLEU 319>.A<OXT 20>
Creating new UNIT for residue: DP sequence: 320
Created a new atom named: 1 within residue: .R<DP 320>
Created a new atom named: 2 within residue: .R<DP 320>
Created a new atom named: 5 within residue: .R<DP 320>
Created a new atom named: 4 within residue: .R<DP 320>
Created a new atom named: 3 within residue: .R<DP 320>
Created a new atom named: 9 within residue: .R<DP 320>
Created a new atom named: 8 within residue: .R<DP 320>
Created a new atom named: 7 within residue: .R<DP 320>

I attached my pdb file.

Thanks for your patiente and looking forward for suggestions.

Best Regards,
Urszula Uciechowska

MSc.PhD Student
Medicinal Chemistry Group
University of Halle-Wittenberg


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