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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