I am trying to dock a domain into a dimer protein. The domain is lowest score structure that was generated by abinition relax. Because they are continous amino acid sequence, so i use atompair constraint betwen c terminal of first monomer with n terminal of predicted domain. I also constraint its c terminal with n terminal of the second mononer.
The problem is the distance between 2 pair of Ca atom is too big to satisfy the constraint condition. The job can not return the out put file. Does anyone have experience about this issue. Would you please teach me how to slove this.
Thank you so much.
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Docking with constraint