On Thu, Dec 13, 2018, Núbia Prates wrote:
>
>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.
I'm not sure I see the line you are referring to, but (as you note)
there is no connectivity information in PDB files, so graphical programs
have to make guesses, which may sometimes be wrong.
You can use parmed to check for the presence/absence of bonds between
the chains in the prmtop file. That's the source of info Amber really
uses.
....dac
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Received on Thu Dec 13 2018 - 10:00:02 PST
