I am trying to use the antibody utinity to modeling a camelid antibody (vhh). I used the antibody.linuxgccrelease to produce 10 relaxed models for this vhh sequence. Then I moved to do the H3 modeling. The "antibody_H3.linuxgccrelease --help" command shows many options for the antibody_H3.linuxgccrelease. However, I am a bit confused about the antibody_H3.linuxgccrelease options.
(1) The"-camelid" and the "-camelid_constraints" options. I think I should add this "-camelid" option in the "flags" file, but actually the program can run without this option. So is it neccessary when working with camelid antibody? And is the "the "camelid_constraints" option neccessary? when should it be used?
(2) The "-l" and the "-nstruct" options. I want to do H3_modeling for the 10 models generated by antibody.linuxgccrelease, so I used "ls grafting/*.relaxed.pdb > grafted_models.list" to get a list, which looks like:
And I included the "-l grafted_models.list" option in the "flags" file. According to the disccussion in the forum, I learned that at least 1000 modeled need to be produced in the H3_modeling for one initial template. So for the "-nstruct" option, should I pass 1000? Since there are 10 initial models, should the value be 10,000?
(3) The "antibody:constrain_cter" and "constraints:cst_weight" options. I guess these two options are both neccessary for vh-vl and vhh antibodies, aren't them? How should the value for the "constraints:cst_weight" option be determined?
(4) The "antibody:auto_generate_kink_constraint" and "antibody:all_atom_mode_kink_constraint" options. Are they necessary for the vhh?
(5) The "antibody:constrain_vlvh_qq" option. This option should not be included for the camelid antibody, should it?
Thank you very much!