I am carrying out energy minimization of the protein peptide complex. But even
after using nstcomm=1 and/or pbc=xyz, my energy minimized structure has peptide
far away from the binding site. This did not happen with ATP-protein complex.
Even in Drug-enzyme tutorial, similar .mdp file is given for energy
minimization. What could be possible reasons for such flying away of the
peptide ? How should I fix the problem ?
Regards,
Nikhil
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