Hi Gromacs users, I am studying antigen-antibody interaction at protein level. I have a protein sequence (no crystal structure, length 180 residues) of the antigen, and have predicted the secondary structure of it (and modeled). By performing conserved domain search using inferno and NCBI I found out a domain in the antigen - PCC1 (residue 90 to 160). I am interested to know how the antigen interacts with the antibody (2000 residues) *in silico*. The ultimate aim is to find out "how the antigen interacts with the antibody, and predict the possible domains used by the antigen to interact with the antibody". I would really appreciate your valuable suggestions on how this can be done using GROMACS MD. Please let me know if I need to provide any further information. Thanks for your time.
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