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

From: Anthony Bogetti <anthony.bogetti.gmail.com>
Date: Tue, 9 Jul 2019 11:40:58 -0400


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


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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