Docking

Hi Rosetta guys:)
Question about seemingly odd behaviour going from local rosetta run (rosetta_2014.16.56682_bundle) to mpi (2014.20.56383.mpi) and of course a slightly newer version of Rosetta3.5 though both are 3.5.

My normal docking scripts contains the flag
-residues:patch_selectors CENTROID_HA

this script runs smoothly.
When running on mpi I can do regular docking, but when introducing this flag (need it for SAXS runs), rosetta tells me that there is no such command on the top level.

Hi all,

I have a quick question:
i have submitted 5 antibody sequences to Rosie and for each of them got ten lowest-energy structures. I have the solved structure of a protein X. I read the paper of Snugdock, got excited by the idea of using snugdock with ensembledock together and now want to perform a docking of my protein X using the models i got from Rosie.

Hi guys

Our local cluster has recently ,finallly, helped me to get the mpi Rosetta version installed.
RosettaDock seems to be working though I get some error messages. None of which i observe on my local computer.
1st:
Created 6242 residue types
Number of residue types is greater than MAX_RESIDUE_TYPES. Rerun with -override_rsd_type_limit. Or if you have introduced a bunch of patches, consider declaring only the ones you want to use at the top of your app (with the options) with the command option[ chemical::include_patches ].push_back( ... ).

Hi,
I have a set of outputs conformation from rosetta after hotspot placement. It's a docking of antigen and antibody. So, how should i evaluate the results? I filtered out the top100 lowest ddG, but, when proceeding to SASA, shape complementarity score and number of hydrogen bond, the results varied. Some having more H-bond with lower Sc score ( around 0.3-0.4). Some with no H-bond but better Sc score.

For example:
A: -31 ddG, 3 H-bond, 2641 SASA, 0.565 Sc
B: -29 ddG, 0 H-bond, 2050 SASA, 0.610 Sc
C: -20 ddG, 5 H-bond, 2039 SASA, 0.323 Sc