Re: [AMBER] WARNING: There is a bond of 8.894214 angstroms between

From: Bill Ross <>
Date: Mon, 26 Apr 2010 10:23:21 -0700 (PDT)

> > Thank you for reply Sir. These two atoms are not supposed to have any bond
> > between them. Initially there were two HO3 atoms present in original pdb,
> > whereas after converting the prmtop to pdb there is only one HO3 atom and
> > the other has changed to O3. I have no clues what to do.
> Assuming you had duplicate HO3 atoms in a residue, probably only one
> was used and an O3 that was in the amber residue template was added.
> If your residue shouldn't have an O3, you may need to define a new
> residue type - how to do this should be described in a tutorial. For
> this you would need a new residue name, and the residue name in the
> pdb would need to be changed to match.

Another possibility is that the residue in question is supposed
to be a terminal one, in which case it should have a TER 'card' (line)
after it, which would cause the residue to be parsed as the terminal
type so it wouldn't be bonded to the next residue in the file. This
might take care of the added O3.


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Received on Mon Apr 26 2010 - 10:30:06 PDT
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