AMBER Archive (2007)

Subject: AMBER: Known residue, unknown error in teLeap

From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Mon Jul 16 2007 - 14:19:07 CDT

Hello,

In loading a .pdb file for acetylProlineNH2 (PRO and ACE are named as per
the convention in all_amino02.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
literally:
R<CPRO 3>.A<OXT 15>

Thanks in advance,
Neelanjana 

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