- I tried fix_bb script and used a resfile > 1 A NATAA, 2 A NATAA and so on as per sample resfile but it shows an error "core.pack.task.ResfileReader: On line 2, the chain identifier 'NATAA' must be just a single character in [_A-Za-z] (note the chain identifier is case sensitive)." I could not understand it.
-Moreover, is it necesaary to make a resfile having information for indiviudal amino acids. Isn't there any option or flag which can fix the amino acids positions and only repack teh side chains (e.g. at all positions I need same amino acids and don't want sequence to change but prefer to have repacking of their side chains).
- second, I am getting a lot of confusion and trouble between using minimizer and relax. Minimizer is a subpart of relax alongwith 'packer' so there must not be any confrontation between both. For saying, in the past I was using relax on a protein with ligand and metal, in which my ligand was totally debonded (totally messed up) and thrown out of the pocket. Then, I shifted to minmize_with_cst and it worked. This time again, when I am trying the 'relax script' on some new protein using following flag "relax.static.linuxgccrelease -s 1xkk.pdb -nstruct 1 -relax:bb_move false -use_input_sc -relax:default_repeats 1 -extra_res_fa FMM.params -database /home/gnss/singhma/rosetta/software/rosetta_bin_linux_2017.26.59567_bundle/main/database/ -out:level 400 -constraint:cst_file cstfile &" again getting a debonded ligand which looks absurd. However, it works fine if I use minimizer (specifically minimize_with_cst).
Here the ligand used is multiple copies of the crystal ligand with proper bond order and valencies (prepared) as I dont want my ligand to vary too much from its original crystal conformation.
Could you suggest me any solution so that I could use relax protocol of rosetta for my proteins (having ligand and metals). Indeed, I am interested in repacking of protein side chains before any future applications and most importantly I don't want my ligand to enjoy outside the pocket which is commonly happening when i use relax.