On Wed, Apr 11, 2018, Aravind Ravichandran wrote:
> The PDB thus created does not have this thioester bond and instead, the
> C-terminal was attached to the n-terminal of the other protein with an
> unusual huge bond.
PDB files do not ordinarily have bonding information. Exactly what are
you doing to decide that there is a bond between the C-terminus and
N-terminus of the two proteins? Or that the thioester bond is missing?
You can use parmed to interrogate the prmtop file to what bonds are
there. You might also want to check that there is a TER card between
the two protein chains that should not be bonded.
....dac
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Received on Wed Apr 11 2018 - 05:30:04 PDT
