The pdb file was originally a dimer, but we removed one of the chains. We
tried adding in TER line at the end and it didn't fix the issue.
How can I load prmtop and inpcrd files directly into leap?
Thanks,
Anthony
On Tue, Jul 9, 2019 at 11:44 AM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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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> >
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Received on Tue Jul 09 2019 - 09:00:04 PDT
