Re: [AMBER] tLEaP error of the N-terminal OXT atom

From: Carlos Simmerling <>
Date: Sat, 15 Feb 2020 18:34:20 -0500

have you checked to make sure the output from modeller is correct? check
the structure after each step and try to figure out when the problem
happens. it's not clear what is happening since you use several programs

On Sat, Feb 15, 2020 at 2:55 PM Wei-Tse Hsu <> wrote:

> Dear everyone,
> I got an error when using H++ to parameterize a protein-ligand binding
> complex and I got the following error: "FATAL: Atom .R<NASN 107>.A<OXT 17>
> does not have a type. ", which means that the OXT atom (the oxygen atom of
> a terminal residue) of aspargine as the N-terminal residue (residue 107) of
> the ligand does not have a type. Since the C-terminal residue (residue 106)
> of the protein also has an OXT atom, but there was no issue with it, I
> really don't know why I got an error like this. Another weird thing is that
> an asparagine as an N-terminal residue should only have two oxygen atoms,
> but there are three oxygen atoms in the residue. Using VMD to visualize the
> structure, I also found that there is a weird/unreasonable bond between the
> OXT atom and its adjacent atom, which seems to be wrong and should be
> deleted. (The ASN residue was built by MODELLER since it was originally
> missing, but I assume that the structure output by MODELLER should be
> correct). I know that deleting the OXT atom would avoid the error that I
> got from H++, but now I'm very confused about if I should delete it, since
> from the visualization by VMD the OXT atom seemed wrong and should be
> deleted, but deleting that atom also makes me feel unsafe as I thought I
> should not even have gotten this error at the beginning. Does anyone have
> suggestions for this? Thank you so much!
> [image: image.png]
> Best,
> Wei-Tse
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Received on Sat Feb 15 2020 - 16:00:02 PST
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