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I have a homology model that contains a residue insertion and thus a 1:1 residue RMSD calculation cannot be performed. I would like to try the Rmsd RosettaScripts Filter with an alignment file to get the correct C-alpha RMSD calculation. However, I'm not sure how to create this alignment file. I've tried the alignment Grishin file I used for Homology modelling but receive this error:

File: src/protocols/protein_interface_design/filters/RmsdFilter.cc:217

[ ERROR ] UtilityExitException

Dear developers,  

I tried to follow the antibody design protocol from the Nature protocol articles but unfortunately I keep getting the following error when I try it:

core.pose.util: [ ERROR ] Can't find residue type 'UNK' in type set of mode fa_standard

This is my command line: 

antibody.default.linuxgccrelease -ignore_unrecognized_res -fasta antibody_chains.fasta

and this is the content of  ROSETTA_CRASH.log:

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."

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!!!