Dear All :
I met some problems when I try to dock a small molecule to a protein using the command "ligand_dock.linuxgccrelease"
What I want:
repack most of the sidechain of protein, but there are several disulfide bonds in the proteins, and I try to use the Flags '-fix_disulf' to
find the disulfide bonds and use '-norepack_disulf' to freeze the CYS involved in the disulfide bonds. the Flags file includes flowing lines :
-start_from 23.60 35.43 21.41
-start_from 17.13 38.18 14.53
-start_from 23.18 31.04 26.60
the command I use is "/home/mldaet/rosetta_old/rosetta3_source/bin/ligand_dock.linuxgccrelease -database /home/mldaet/rosetta_old/rosetta3_database/ $flags"
the docking results show that the disulfide bonds are not freezed as I want, it also repacked as other side chains. I also tried the flags "-norepack1" as a control
and the results show that that flag seems not working, all the side chain of proteins are repacked. Does this mean the ligand-protein docking in rosetta will consider
all the side chains' repacking by default ? Any suggestions are deeply appreciated !!!
Best Regards to all.