AMBER: Known residue, unknown error in teLeap

From: Neelanjana Sengupta <>
Date: Mon, 16 Jul 2007 12:19:07 -0700


In loading a .pdb file for acetylProlineNH2 (PRO and ACE are named as per
the convention in, I label the remaining as {N,H,H2} and call
it NME ------- to see what it does, I know this is not exactly right), I get
the foll. error:

2 residues had naming problems.
 Residues split, so res numbers will not correspond to pdb.
Created a new atom named: H2 within residue: .R<NME 1>
  Added missing heavy atom: .R<NME 1>.A<CH3 3>
  Added missing heavy atom: .R<CPRO 3>.A<OXT 15>
  total atoms in file: 23
  Leap added 5 missing atoms according to residue templates:
       2 Heavy
       3 H / lone pairs
  The file contained 1 atoms not in residue templates

I do understand the lines 3 to 5. I do NOT understand why a missing atom had
to be added to PRO, as the naming and connectivity are exactly as in
PROline. Also, what is 'CPRO', and what does this type to message mean
R<CPRO 3>.A<OXT 15>

Thanks in advance,

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Received on Wed Jul 18 2007 - 06:07:31 PDT
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