I would like to use "loopmodel.linuxgccrelease" to remodel an internal loop of my heavy chain (HC). It works all fine except one defect: there are some coordinates shift between the output and the input. As I will finally combine light chain (LC) structure and heavy chain (HC) structure into one PDB file, these coordinates change will make the distance between LC and HC not the same as before. Can I ask how to solve this?
The input PDB and out PDB as well as the options files are attached.
My command line is:
~/Cheng/rosetta_2014.30.57114_bundle/main/source/bin/loopmodel.linuxgccrelease @/mnt/hgfs/Mutagenesis_Rosetta/4KMT/4.0_loop_modeling/loop.options -database ~/Cheng/rosetta_2014.30.57114_bundle/main/database >& /mnt/hgfs/Mutagenesis_Rosetta/4KMT/4.0_loop_modeling/loop.log &
Thank you very much.