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Speeding up docking to a large complex

Greetings,

I would like to dock a small protein (59 amino acids plus one 140 atom ligand) to a large trimeric complex (358 amino acids *per monomer*, plus eight 140-atom ligands). The total number of atoms in the system is nearly 21,000.
When I run a small test of the system using the following flags (we use Torque for queuing jobs) and generate 10 decoys per instantiation, each decoy takes between 1800 and 2400 seconds to complete (30-40 minutes).
command:
/pathto/bin/docking_protocol.linuxgccrelease
flags:
-in:path /pathto/rosetta_database/

Post Situation: 

Creating centroid patches for Proline (pro_hydroxylated_case1 and pro_hydroxylated_case2)

Greetings,

When trying to dock two proteins (with ligands), I obtained the following error:

can not find a residue type that matches the residue PRO_p:pro_hydroxylated_case1at position 31

ERROR: core::util::switch_to_residue_type_set fails

ERROR:: Exit from: src/core/util/SwitchResidueTypeSet.cc line: 135

When I review the log file, I see the following:

protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 4219 residue types

Post Situation: 

ddg_monomer conformational search...

Hi,
I'm fairly new to using Rosetta suite, so sorry if silly questions. I'm running ddg_monomer app for a protein of about 150 aa.

A) the pdb outputs I get are all the same, there is no backbone or sidechain movement neither for wt nor for mut structures (50 for each as recommended). I intended to carry out the protocol of row 16 in Kellogg, 2011. I attached the options file, if you'd be so kind to take a look at it. What am I missing here?

Post Situation: 

Unpredictible amino acid replacements

During loop modeling using loop_modeling.py from http://www.pyrosetta.org/scripts
and using my frag3 file for my protein I found that unpredictable amino acid replacements occur for my protein.
Could you please tell me why it is happened and how to avoid this situation,
as I do not want to change my amino acids during loop modeling.

Thank you,

Victor

Post Situation: 

Problems with boost

Short story:

I get a segmentation fault when I issue:

from rosetta import *

in function PyInt_FromLong. But I am not sure what is wrong, since PyRosetta compilation worked fine.

Long story:

The binary distribution PyRosetta.MacOSX.SnowLeopard-r48781.64Bit works on my computer with the system python 2.6.1, but I would like to compile a version for the EPDPython 2.7, which I normally use. Also, I thought of this as training for a compilation on an older Centos system, for which there is no binary distribution.

I have:
-Mac OS X 10.6.8 32bit

Post Situation: 

symmetric docking application rosetta3.2: the docking_local_refine flag

Hi,
I have 2 questions regarding the high resolution stage of the symmetric docking application in rosetta3.2:
1. What exactly are the changes performed to the structure by the docking_local_refine flag (The reason I am asking this is that I want to know which clustering radius to use on the outputs and since I don't use the perturb_rigid_body_dofs flag in this stage I don't know how to set the radius for this clustering)?

Post Situation: 

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