Reply To: high resolution protein docking doesn’t work

[Anonymous]

it seems to work for the test and I found the new generated docking result is different from input structure. However, when I don’t know why use the high resolution protocol, it still doesn’t work.

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here is the command in terminal

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test/integration> python integration.py docking -d /soft/rosetta3.1/database
Running docking on localhost …
Finished docking in 18 seconds

Just generated ‘ref’ results; run again after making changes.
test/integration> python integration.py docking -d /soft/rosetta3.1/database
Running docking on localhost …
Finished docking in 31 seconds

FAIL docking
Files ref/docking/1brs_0001.pdb and new/docking/1brs_0001.pdb differ
Files ref/docking/1brs.fasc and new/docking/1brs.fasc differ
Files ref/docking/flags and new/docking/flags differ
Only in new/docking/input: relax.pdb
Files ref/docking/log and new/docking/log differ
Only in new/docking: relax_0001.pdb

1 test(s) failed. Use ‘diff’ to compare results.

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Here is my flag for high resolution:

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-in
-file
-s 08.pdb
# the input file should have two single, complete chains A and B
# for Ab molecules (with L+H chains) use -docking::partners flag below
-path
-database /soft/rosetta3.1/database
# customize this to point to your installation directory
-docking
# very small perturbations occur in the absence of any docking flags
-docking_local_refine
-dock_pert 3 8
# do a small perturbation with partner2: -dock_pert DEGREES ANGSTROMS
#-spin
# rotate partner2 about the intermolecular axis
-dock_min
# Minimize the final fullatom structures. default=’false’
#-partners
# defines the docking partners by ChainID; see manual
-out
-nstruct 10
# this should be set to a large number for effective sampling
-mute core.util.prof
# reduces copious output, without overdoing as with -mute all
-file
-o dock_output2
# scorefile will be named dock_output2.sc (or .fasc for fullatom)
-fullatom