Docking

Hi all
I am docking several different proteins and before docking I use fastrelax to relax the individual proteins.
Fir some of the proteins (they are all less than 200 aa) Fastrelax takes extreemly long to generate 25 poses.
For one in particular following error pops up:

I am currently trying to set up a docking run between two proteins that have compatible symmetry, and almost certainly interact along a 3-fold symmetry axis. One molecule is trimeric, the other is a D3 hexamer, with protomeric MWs of 20 and 25 kDa respectively. I have experimental (x-ray) structures for both proteins, and an initial model where the two proteins are in contact, and lined up with the 3-fold axis of each along Z. I therefore want to search only rotations around Z, along with a small Z-translation shift.

Dear all,
I have submitted a couple of protein-protein docking (docking2) jobs.
I have received the confirmation mails but the results aren't accessible, even if i can see them in my queue list as "Finished". I Suppose they are not failed aas i would expect a "Failed" status, but i got this "Error 500 - We're sorry but we weren't able to process this request." reply.

How can I fix it?

Thank you

Andrea Coletta (Sherpaman)

Hi,
I'm new in rosetta docking. I ran this command
/farm/software/rosetta3.5/rosetta_source/bin/rosetta_scripts.linuxgccrelease -database /farm/software/rosetta3.5/rosetta_database/ -run:constant_seed -run:rng mt19937 -overwrite -no_optH -ex1 -ex1aro -ex2 -mute core.util.prof -mute core.io.database -run:preserve_header -in:file:s RCL+LMP.pdb -extra_res_fa LMP.fa.params -extra_res_cen LMP.cen.params -parser:protocol ligand_dock_LMP.xml -enzdes:cstfile LMP.cst -nstruct 3 > output.log
and it was stopped by
ERROR: set_atom_base: atoms must be bonded!