Dear Charles,
Thank you for the previous replies. I now need to confirm the allowed space for
MTSL side chain to move freely. In the other words, after calculated structure
with NOE restraints, I substitute a specific residue to CYSP with addatoms.py.
Since the generated structure might not be at its lowest energy state and the
MTSL side chain could sample a large space, I am thinking about doing energy
minimization with fixed backbone atoms. The process should be similar with the
preminimization step in AMBER. Which script should I use? Or can I just comment
out the restraints and heat-cooling part of the original 'anneal.py' script,
then fix the backbone atoms?
Also, is there a simple way to convert MTSL or CYSP parameters (topology, bond,
charge, etc.) to AMBER?
Thank you very much for your help!
Best wishes,
Yi Zhang
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