Pratul,
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.
Nubia
________________________________
De: Pratul Agarwal <pratul.agarwal-lab.org>
Enviado: quinta-feira, 13 de dezembro de 2018 15:25
Para: AMBER Mailing List
Assunto: Re: [AMBER] strange line between protein chains
Nubia,
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
Pratul K. Agarwal, Ph.D.
(Editorial Board Member: PLoS ONE, Microbial Cell Factories)
Web: http://www.agarwal-lab.org/
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?
Cheers,
Nubia
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Received on Fri Dec 14 2018 - 05:00:02 PST
