Re: [AMBER] There is a bond of 8.882728 angstroms between: [Blank]

From: Carlos Simmerling <>
Date: Tue, 9 Jul 2019 11:43:42 -0400

you might try to load in the prmtop and inpcrd generated by leap, since
that will show the bonds leap determined.
could you have a dimer without a TER line?

On Tue, Jul 9, 2019 at 11:41 AM Anthony Bogetti <>

> Hello,
> I'm trying to create a topology and coordinate file for a protein in leap.
> I obtained the pdb file and added hydrogens and changed nothing else. When
> I load the pdb file in tleap, everything seems fine but I'm getting an
> error message that says:
> There is a bond of 8.882728 angstroms between: [Blank]
> It doesn't tell me what atoms this "bond" is between. What could be
> causing this?
> I've visualized my structure and everything looks fine.
> I'm using ff14SB and I've checked all of my atom names/types and they are
> correct.
> Thanks,
> Anthony Bogetti
> Graduate Student at University of Pittsburgh
> Advisor: Dr. Lillian Chong
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Received on Tue Jul 09 2019 - 09:00:02 PDT
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