Re: [AMBER] strange line between protein chains

From: Núbia Prates <>
Date: Fri, 14 Dec 2018 12:54:40 +0000


I rendered the image in sticks/lines and this strange line was not there.

>From the log file (attached) I could not find anything wrong.


De: Pratul Agarwal <>
Enviado: quinta-feira, 13 de dezembro de 2018 15:25
Para: AMBER Mailing List
Assunto: Re: [AMBER] strange line between protein chains


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?


AMBER mailing list<>

AMBER mailing list

AMBER mailing list

Received on Fri Dec 14 2018 - 05:00:02 PST
Custom Search