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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org<mailto: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 Thu Dec 13 2018 - 09:30:03 PST
