I am using the "antibody_H3" command to model the H3 loop of antibodies according to the guide at https://www.rosettacommons.org/docs/latest/application_documentation/antibody/antibody-protocol.
The "-nstruct" option there is 1000. According to the guild, building one model needs 1 cpu hour. That means in my 12 cpu work station, to build 1000 model will need ~84 hours. If I wish to model more antibodies, say, like 1000 or more, the time consumed would be unacceptable. So I wonder whether I could reduce the "-nstruct" option to 100 or 20 but can still select a rational structure among these models? Does any one has the concept at least how many models have to be generate to get the correct structure for an antibody?
Thank you very much in advance.