Hi everyone,
I have some problems about protein and protein docking. I want to dock a peptide into protein using global docking. But there are some carbohydrates in my protein. After docking, the site of the protein bonds with carbohydrate and the carbohydrates bond each other have some error. And the score of the results are very high.
Generally, they should automatically dehydrogenate after docking. Did I miss some commands or how can I solve this problem?
I attach the output’s image and following is my flag:
-in:file:s input_files/test.pdb
-nstruct 1
-include_sugars
-partners A_B
-randomize1
-randomize2
-center_at_interface
-ex1
-ex2aro
-out:path:all output_files
-out:suffix _global_dock
Thanks in advance
Shu
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