I modeled a camelid antibody structure with "antibody.linuxgcc.release" from its fasta sequence. However, after aligning the modeled structure to its crystal structure, I found that there are obvious difference between the H1 region of these two structures (Please see the attached figure). I wish to use this model to predict the structure of the antibody in complex with an antigen with "docking_protocol.linuxgcc.release". I guess this difference may affect the accuracy of the predicted complex structure.
The H3 region structure can be optimized with "antibody_H3. linuxgcc.release", but is there a way to optimize the H1 and H2 regions? Can "relax.linuxgcc.release" be used for H1 and H2 optimization? If it can, how to set the options?
Thank you in advance!