I want to run a relaxation on a protein structure that I've got already. It's a membrane protein so I wanted to be able to use the relax application but with the membrane scoring functions and scoring weights from the membrane ab initio application.
I've tried running relax mode, specifying the scoring weights to be 'score_membrane.wts'; the command line I used is shown below:
''relax.linuxgccrelease -database /usr/dunn/software/rosetta/rosetta_database/ -relax:fast -score:weights score_membrane -out:pdb -out:prefix fast_memb_test -out:nstruct 1 -in:file:s input_files/1OKC.clean.pdb''
but this generated a segmentation fault after the line:
''protocols.relax.SimpleMultiRelax: Running FASTRELAX fast_memb_test1OKC.clean_0001''
I had a look at the apply function in SimpleMultiRelax - one of the things that is done just after that ouput line is generated is that the original pose is scored, so this is most likely the problem, but I don't know what to do about it.
First of all, is it even possible to use the membrane scoring functions in this context and then, if so, what inputs should I give?