On Tue, May 07, 2013, javier alejandro rendon carrillo wrote:
> Created a new atom named: P within residue: .R<DC5 192>
This means that your pdb file has a P atom in residue 192, but the DC5
template library doesn't have such an atom. You have to make the atoms and
residues in the PDB file match that in the library, by changing either one or
the other.
[Developers...can someone put an extended error message into LEaP when
this happens? It is almost always a fatal error, but "Created new atom"
doesn't sound very bad.]
> Added missing heavy atom: .R<DA3 202>.A<C5' 5>
> Added missing heavy atom: .R<DA3 202>.A<C4' 8>
> Added missing heavy atom: .R<DA3 202>.A<O4' 10>
> Added missing heavy atom: .R<DA3 202>.A<C3' 27>
> Added missing heavy atom: .R<DA3 202>.A<C1' 11>
> Added missing heavy atom: .R<DA3 202>.A<C2' 29>
> Added missing heavy atom: .R<DA3 202>.A<O3' 32>
> Added missing heavy atom: .R<DA3 202>.A<N9 13>
> Added missing heavy atom: .R<DA3 202>.A<C8 14>
> Added missing heavy atom: .R<DA3 202>.A<C4 26>
> Added missing heavy atom: .R<DA3 202>.A<N7 16>
> Added missing heavy atom: .R<DA3 202>.A<C5 17>
> Added missing heavy atom: .R<DA3 202>.A<N3 25>
> Added missing heavy atom: .R<DA3 202>.A<C6 18>
> Added missing heavy atom: .R<DA3 202>.A<C2 23>
> Added missing heavy atom: .R<DA3 202>.A<N6 19>
> Added missing heavy atom: .R<DA3 202>.A<N1 22>
Here you have atoms in the template that are missing in the pdb file. Having
so many is pretty serious, and will almost certainly give you bad results.
Check the atoms and residues carefully in your input PDB file.
...good luck....dac
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Received on Tue May 07 2013 - 06:00:02 PDT
