How to add additional rounds of design and optimization in Rosetta scripts?

Hello,

I am using RosettaLigand design protocol to design protein binders for a small molecule. The tutorial I referred to is Mr. Rocco Moretti’s paper ( Methods Mol Biol. 2016 ; 1414: 47–62. doi:10.1007/978-1-4939-3569-7_4.).

According to the tutorial, “the provided protocol only does one round of design and minimization. Additional rounds may be desired for further refinement. Simply replicate the low_res_dock, design_interface, and high_res_dock lines in the PROTOCOLS section to add additional rounds of design and optimization.“

I am not sure if it’s correct to write like this, two runs for example.

…

<PROTOCOLS>

        <Add mover_name=”favor_native”/>

        <Add mover_name=”low_res_dock”/>

        <Add mover_name=”designinterface”/>

        <Add mover_name=”high_res_dock”/>

        <Add mover_name=”low_res_dock”/>

        <Add mover_name=”designinterface”/>

        <Add mover_name=”high_res_dock”/>

        <Add mover_name=”add_scores”/>

    </PROTOCOLS>

…

Any suggestion will be appreciated!

Nicole

2020/11/04