AMBER Archive (2006)

Subject: AMBER: leap - how to recognize my structure

From: sethl_at_gatech.edu
Date: Thu Sep 07 2006 - 17:16:06 CDT

Dear Amber Community,

I'm not sure exactly what it means to have "unique atom names" but in my pdb I
changed the atom names for my ligand so that no two atoms would have the same
name by C1, C2, C3, C4, C5... etc since my ligand is a proflavine molecule only
having 13 C's and 3 N's. Like so:

ATOM 1 C1 UNK 0 0.914 -7.130 22.096 0.00 0.00
ATOM 2 C2 UNK 0 -0.349 -7.102 21.604 0.00 0.00
ATOM 3 C3 UNK 0 -0.597 -6.916 20.236 0.00 0.00
ATOM 4 C4 UNK 0 0.430 -6.755 19.336 0.00 0.00
ATOM 5 C5 UNK 0 1.762 -6.775 19.791 0.00 0.00
ATOM 6 C6 UNK 0 4.037 -6.637 19.357 0.00 0.00
ATOM 7 C7 UNK 0 4.357 -6.827 20.776 0.00 0.00
ATOM 8 C8 UNK 0 5.707 -6.838 21.182 0.00 0.00
ATOM 9 C9 UNK 0 6.689 -6.673 20.261 0.00 0.00
ATOM 10 C10 UNK 0 6.394 -6.490 18.903 0.00 0.00
ATOM 11 C11 UNK 0 5.097 -6.471 18.446 0.00 0.00
ATOM 12 C12 UNK 0 3.322 -6.993 21.699 0.00 0.00
ATOM 13 C13 UNK 0 2.009 -6.970 21.223 0.00 0.00
ATOM 25 N1 UNK 0 2.774 -6.620 18.941 0.00 0.00
ATOM 26 N2 UNK 0 7.439 -6.327 17.996 0.00 0.00
ATOM 27 N3 UNK 0 -1.913 -6.896 19.780 0.00 0.00

When I load my prep files then load the pdb there are a couple errors
associated with the ligand molecule:

One sided connection. Residue: missing connect1 atom.
Created a new atom named: C13 within residue: .R<UNK 25>
Created a new atom named: N3 within residue: .R<UNK 25>
  Added missing heavy atom: .R<UNK 25>.A<C 1>
  Added missing heavy atom: .R<UNK 25>.A<N 8>
  total atoms in file: 529
  Leap added 281 missing atoms according to residue templates:
       2 Heavy
       274 H / lone pairs
       5 unknown element
  The file contained 2 atoms not in residue templates

I believe this problem has a simple solution but is right now beyond my
understanding. Thanks for your help in advance.

Thanks,
SETH
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