AMBER Archive (2006)

Subject: Re: AMBER: leap - how to recognize my structure

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Thu Sep 07 2006 - 17:34:09 CDT

the names in the PDB file and your residue library need to match.
two of the atoms don't- it found 2 atoms that it doesn't know about
and added two atoms that were not in the pdb. these are probably the
same 2.

be very careful with the renaming to make sure that the atoms match up
properly. leap won't warn you if all atoms are present but not in the
right places. in other words, the atom coordinates must be right for
the specific atom types. the names are just a way to match them up
between library (with types and parameters) and pdb file (with coordinates).

sethl_at_gatech.edu wrote:

>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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