Here's the pdb file with ACE and NME terminal groups added.
Anthony
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 - 09:00:04 PDT
