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
<InitializeFromCommandline name=ifcl />
<RestrictToRepacking name=rtr />
<FastRelax name=relax repeats=8 scorefxn=score12 task_operations=ifcl,rtr />
<Add mover=relax />
$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 and am particular interested in what this error mean. I have tried changing the B factor to 1 and removing the extra column with information but it does not help..
I would greatly appreciate any comments.