sorry I meant to visualize your prmtop and crd in something like VMD.
On Tue, Jul 9, 2019 at 11:49 AM Anthony Bogetti <anthony.bogetti.gmail.com>
wrote:
> 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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Received on Tue Jul 09 2019 - 09:30:02 PDT
