Dear Amber users,
I have a problem with MD simulations of a small enzyme with its substrate.
When I use iwrap=1 option and the half of the substrate in the complex
crosses in the next simulation box the option automatically puts the
substrate in the center of the box without the enzyme. Eventually, after a
few ps the enzyme comes to the center also and the complex is made again.
Is there an option in cpptraj which can generate a full trajectory of an
enzyme with its substrate in active site? I trayed with the center option
in cpptraj, but no luck...
Sincerely,
Andrea
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Received on Tue Oct 22 2019 - 03:30:03 PDT
