Design

Hello all, I am using the antibody.mpi.linuxgccrelease to model multiple antibodies. Most work fine but about 10% are failing with weird error messages.  I have tried everything to figure out the problem but am having no luck. These antibodies are clinical molecules, and so I feel like my failure rate is pretty high, and I'm probably doing something wrong.  There is not a lot of documentation about the (newer) antibody homology modelling application and so I am a little bit at a loss as what to do to make the program more robust. Thanks as usual for all your help!!!

Hello,

I am following the protein design steps presented in the Dr Mieler lab. One of the steps is to generate resfile with  define_interface.py script. I checked my rosetta/tools/protein tools/scripts path, but there is not such a file. Where can I find this script?

Thank you

I am trying to design a helical linker between two strongly interacting subunits that connects their termini using RosettaRemodel.

I am running remodel with the following flags in mpi mode and get the desired output (around 2-4 structures with -num_trajectory 32). However when I increase -num_trajectory to e.g. 1000 I still get only around 2-4 strucures out (named 1.pdb 2.pdb ...). while computation time increases drastically.

Good evening, I want to use the pepspec anchor dock application and I am using the following flags file:
-ignore_unrecognized_res
-pepspec :: no_prepack_prot
-pepspec :: anchor_type PRO
-pepspec :: prep_align_prot_to input / 1CKA.nopep.pdb
-s input / 1CKA.nopep.pdb
-pepspec :: ref_pdb_list input / homol.pdblist
-restore_pre_talaris_2013_behavior
-score :: weights pre_talaris_2013_standard.wts
-pepspec :: soft_wts soft_rep.wts
-pepspec :: interface_cutoff 6
-pepspec :: n_dock_loop 1