I am new to rosetta. I am trying to build the missing residue loops in 4hna sturcture. But I am getting error while generating the input file for the loopmodel application.
My input command is: loops_from_density.linuxgccrelease -database /util/rosetta/rosetta-3.2/rosetta_database/ -in:file:fullatom 4hna_9_his.pdb -edensity::mapfile apo_cut12.mrc -edensity::whole_structure_allatom_wt 1.0 -edensity::realign min -edensity::sliding_window 9 -edensity::mapreso 8.9 -edensity::grid_spacing 2.12 -max_helix_melt 1 -max_strand_melt 1 -frac_loop 0.026
I am getting the error message: ---> ERROR: Unused "free" argument specified: 4hna_9_his.pdb
But this is just my input pdb structure not any library function. Any suggestion is welcome. Please help.
-in:file:fullatom is a Booloean flag - it's either on or off, and doesn't take a filename. To pass an input PDB file in, you'd use the -in:file:s option, so your commandline should be "... -in:file:fullatom -in:file:s 4hna_9_his.pdb ..."
Thanks for your reply. Now the problem is with flags -max_helix_melt and -max_strand_melt. If I take the default values (-1), it is creating the loopfile with no LOOP information. How should I determine this to get the correct loopfile.