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 <anthony.bogetti.gmail.com>
wrote:
> 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
