Do you have a TER 'card'/line between your chains?
If the line exists as a bond in AMBER (i.e. in the prmtop), leap would
have warned about a long bond on saveamberparm or maybe check.
Bill
On 12/13/18 7:20 AM, Núbia Prates wrote:
> Dear Amber users,
>
> I am trying to simulate a protein-protein complex with AMBER16. After preparation with tleap I looked the pdb file using ambpdb and I have been seeing a line connecting the chains (figure attached). The pdb file load in tleap have no connection records.
>
> Can anyone help me to understand what is the problem, so I can fix it?
>
> Cheers,
> Nubia
>
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Received on Thu Dec 13 2018 - 10:30:01 PST
