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

From: Bill Ross <>
Date: Mon, 26 Apr 2010 10:19:28 -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.


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Received on Mon Apr 26 2010 - 10:30:05 PDT
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