Dear all,

I have a questions concerning MD free energy calculations using alchemical tranformation. I want to restrain the backbone of my protein which I mutate during TI. However, I do not know how to correctly generate position restrains. If I use the position restrain file, which I generated for the A state, following warning shows up:

WARNING 1 [file posre.itp, line 1470]:
  Some parameters for bonded interaction involving perturbed atoms are
  specified explicitly in state A, but not B - copying A to B

Can I ignore this warning, or do you have any suggestions for me?

All the best and thank you very much in advance

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