I am using Rosetta 3.3, ddg_monomer application. I am trying to reproduce protocol 19 from Table I (Kellog, 2010) but it looks like there is no backbone minimization at all. In Fig. 3 there is a visible backbone movement but in my case it behaves like in supplementary material Fig. 1, where no backbone movement is observed.
First off, you repeat a number of options. For example, you have -ddg:min twice, once false and once true. The latter should override the former, but for best results I’d only specify it once.
Your core problem is that you haven’t specified ‘-ddg:sc_min_only’. By default it’s true, and if you want more than just sidechain minimization (i.e. you want the backbone to move) you need to explicitly set it false.
(By the way, I’d recommend taking a look at the Kellogg et al. supplemental information – it gives example commandlines for most of the protocols in the table.)
Thanks for quick answer. Adding the -ddg:sc_min_only was one of the problems. I was using also wrong weight file (soft_rep instead of soft_rep_design). So supplemental information was realy usefull.
Thanks a lot, best regards