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

From: David Cerutti <dscerutti.gmail.com>
Date: Tue, 9 Jul 2019 11:44:19 -0400

Can you attach your PDB file? Usually this sort of thing is the result of
a missing TER card.


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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jul 09 2019 - 09:00:03 PDT
Custom Search