I use AbinitioRelax.linuxgccrelease to generate the structures with the flag -out:file:fullatom. My comman is like : AbinitioRelax.linuxgccrelease -in::file::fasta seqt_.fasta -in:file:frag3 aaseqt_03_05.200_v1_3 -in:file:frag9 aaseqt_09_05.200_v1_3 -run:constant_seed -run:jran 1111111 -database /ifs/ibfs3/data/bbarz/NIH/rosetta3.1/rosetta_database -out:pdb -out:file:fullatom -out:nstruct 2
But why do I still get the centroid mode pdbs ( with CEN atom in it, but not fullatom ) ? How can I fix it and make it generate fullatom pdbs? Thank you very much!
I was able to generate the full atom mode. Use the relax mode.
the relax mode is working fine. I am now able to convert cantroid mode to full atom mode by giving relax.linuxgccrelease -database path_of_rosetta_database -s input_pdb_wth_CEN_atoms -relax:fast.
This worked well, but takes 20 min to do the job for 1 pdb file.
more information @ http://www.rosettacommons.org/manuals/archive/rosetta3.1_user_guide/app_...
I hope ths solves the problem.