I have meet some problem when simulating a protein and ATP complex. The energy minimization will stop after 14 steps. I had followed Mark's suggestion, did the protein and ATP eneryg minimization independently, and found that the protein can finish its minimization correctly, but the ATP 's minimization stopped after 14 steps. So it seems that there are something wrong with ATP. And Mark also said "Probably your topology is broken", what is it means? What should I do now?
Best wishes!
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