Fastrelax problem

[Anonymous]

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:

core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating LinearMemoryInteractionGraph
core.pack.pack_rotamers: built 9099 rotamers at 245 positions.
core.pack.pack_rotamers: IG: 7504384 bytes
core.optimization.Minimizer: reset HESSIN from failed line search
HESSIN for (i,i): 1 1.21939
G for (i): 1 -1.63693e-06
HESSIN for (i,i): 2 1.0625
G for (i): 2 -0.000937159

Rosettascript:
“












“

flags:
-in:file:fullatom
-out:file:fullatom
-ignore_zero_occupancy false
-linmem_ig 10
-ex1
-ex2
-use_input_sc
-corrections:score:use_bicubic_interpolation true

$direxe/rosetta_scripts.default.linuxgccrelease @relax.flags -restore_pre_talaris_2013_behavior -s $dirunbound -parser:protocol relax_saxs.xml -nstruct 25 -database $dirdata >& relax.log

I was wondering if B-factors can influence the speed of Relax?

To note all proteins has been cleaned and only contain the structure itself.

Last for the particular protein giving extra problems I have attached the PDB.

I would greatly appreciate any comments.

Best

Pernille

[Anonymous]

just realized I posted this the wrong place but cannot figure out how to delete it. Sorry! Has moved under applications…

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