Re: AMBER: Known residue, unknown error in teLeap

From: David A. Case <>
Date: Mon, 16 Jul 2007 18:32:16 -0700

On Mon, Jul 16, 2007, Neelanjana Sengupta wrote:
> 2 residues had naming problems.
> Residues split, so res numbers will not correspond to pdb.

This usally means that you had a set of atoms that were all in residue "n",
but these atoms did not all have the same residue name. LEaP tries to figure
out a decent solution to this problem, but you are better off fixing the pdb
file, so that residue names and numbers are consistent.

> Created a new atom named: H2 within residue: .R<NME 1>
> Added missing heavy atom: .R<NME 1>.A<CH3 3>

This is quite odd: NME is a C-terminal residue, but you seem to have NME
as the first residue in the protein. I don't see how this can work.

> Added missing heavy atom: .R<CPRO 3>.A<OXT 15>

"CPRO" just means a C-terminal proline, that is, it thinks that PRO is the
last residue in the protein. It sounds like this is not what you want.
Again, the fix is to edit the input pdb file so that is really what you want
it to be.

...good luck....dac

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Received on Wed Jul 18 2007 - 06:07:35 PDT
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