Re: [AMBER] strange line between protein chains

From: Pratul Agarwal <>
Date: Thu, 13 Dec 2018 17:25:19 +0000


This could be a visualization software issue rather than ambpdb/tleap/xleap issue. I have noticed that recent versions of PyMOL, for example, does connect two chains in a similar way to your image. Can you render the image in sticks/lines? See if it still there.

The more rigorous way to check this will be to look at the leap.log file and see if the N-terminal and C-terminal residues were correctly modified for the two chains.


Pratul K. Agarwal, Ph.D.
(Editorial Board Member: PLoS ONE, Microbial Cell Factories)

On 12/13/2018 10:20 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?


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Received on Thu Dec 13 2018 - 09:30:03 PST
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