AMBER Archive (2008)

Subject: Re: AMBER: protein-ligand complex problem

From: David A. Case (
Date: Thu Apr 10 2008 - 18:51:55 CDT

On Fri, Apr 11, 2008, Lynn wrote:

> Created a new atom named: NE2 within residue: .R<GLH 71>
> Added missing heavy atom: .R<GLH 71>.A<OE2 13>
> -------------------------
> But I changed GLN71 to GLH71, the error still exist.
> The attached 2Fmo1.pdb run well ,but 2Fmo2.pdb did not.

The message doesn't appear to have anything to do with ligands, or their
names. In the "2Fmo2.pdb" file, residue 71 is GLH, which is a protonated
glutamic acid. LEaP is (correctly) telling you that you have an "extra"
NE2 atom in the pdb file that should not be there, and that you are missing
an OE2 atom, that should be there.

In the 2Fmo1.pdb file, residue 71 is GLN, which is probably what it should
be. You don't give any reason why you changed GLN71 ro GLH71, but this is
almost certainly *not* what you want to do.

I had trouble understanding your questions about the ligands. Remember, it is
not helpful to just say something "does not run well": you need to say exactly
what commands you issued, and exactly what the resulting messages were.

...good luck...dac

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