How do you refine the native structure?

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    • January 10, 2008 at 4:40 pm #522
      Anonymous

        Hi-
        I am trying to refine the native structure. Currently I idealize the native structure then relax it using the commands below. Unfortunately, this protocol sometimes generates structures high in energy, far from native. Does anyone know the correct protocol?

        idealize:
        rosetta.mpilam aa 1AD6 _ -timer -increase_cycles 1 -new_centroid_packing -idealize -fa_input -s 1AD6.pdb -vary_omega -omega_weight 0.5 -farlx -ex1 -ex2 -short_range_hb_weight 0.50 -long_range_hb_weight 1.0 -no_filters -nstruct 4 -paths /home/brunette/parallel_mbs/proteins/1ad6/paths_native.txt > 1ad6_abinit.log

        relax:
        rosetta.mpilam aa 1AD6 _ -timer -output_pdb_gz -increase_cycles 1 -new_centroid_packing -relax -fa_input -s aa1AD6_0001.pdb -vary_omega -omega_weight 0.5 -farlx -ex1 -ex2 -short_range_hb_weight 0.50 -long_range_hb_weight 1.0 -no_filters -termini -nstruct 100 -paths /home/brunette/parallel_mbs/proteins/1ad6/paths_native.txt > 1ad6_abinit.log

        Thanks for the help, -TJ

      • January 10, 2008 at 4:40 pm #3923
        Anonymous

          Hi,

          Disclaimer: I have not done too much with relax mode but …

          adding -farlx, -farlx -minimize -bb_only, or -minimize -bb_only may help reduce the structural distribution.

          -Glenn

          > Hi-
          > I am trying to refine the native structure. Currently I idealize the native structure then relax it using the commands below. Unfortunately, this protocol sometimes generates structures high in energy, far from native. Does anyone know the correct protocol?
          >
          > idealize:
          > rosetta.mpilam aa 1AD6 _ -timer -increase_cycles 1 -new_centroid_packing -idealize -fa_input -s 1AD6.pdb -vary_omega -omega_weight 0.5 -farlx -ex1 -ex2 -short_range_hb_weight 0.50 -long_range_hb_weight 1.0 -no_filters -nstruct 4 -paths /home/brunette/parallel_mbs/proteins/1ad6/paths_native.txt > 1ad6_abinit.log
          >
          > relax:
          > rosetta.mpilam aa 1AD6 _ -timer -output_pdb_gz -increase_cycles 1 -new_centroid_packing -relax -fa_input -s aa1AD6_0001.pdb -vary_omega -omega_weight 0.5 -farlx -ex1 -ex2 -short_range_hb_weight 0.50 -long_range_hb_weight 1.0 -no_filters -termini -nstruct 100 -paths /home/brunette/parallel_mbs/proteins/1ad6/paths_native.txt > 1ad6_abinit.log
          >
          > Thanks for the help, -TJ

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