Difference between Eres, Ereduce, Enew?

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    • #567
      Anonymous

        I am running:

        command executed: rosetta.gcc -design -resfile 1ubi_.resfile -cluster_design -cluster_size 2 -mutout no_interface.out -n_mutatpos 5 -repack_neighbors -s 1ubi_.pdb

        And get :

        1.
        +

        ENERGY FOR WT STRUCTURE “1ubi_” is -94.6182

        #

        1.

        CONTRIBUTIONS TO THE ENERGY FOR THE WT STRUCUTRE:

        1.

        Eatr Erep Esol Eaa Edun Eintra Ehbnd Epair Eref Eh2o Eh2ohb Eh2osol Eres SASA_pack pdb name
        DG_BIND -219.2 22.1 113.0 -16.8 95.7 0.1 -5.4 -4.6 24.0 0.0 0.0 0.0 -94.62 3.620 1ubi_

        1.
        *

        CHANGES IN ENERGY FOR MUTANT STRUCTURES: MUT-WT

        o

        1.

        Eatr Erep Esol Eaa Edun Eintra Ehbnd Epair Eref Eh2o Eh2ohb Sasa_pack Eres Ereduce Enew N_MUT ROS# PDB# CH WT M NB ROS# PDB# CH WT M NB
        DG_CALC -0.277 0.178 0.417 0.449 -0.316 -0.002 -0.939 -0.178 -0.630 0.000 0.000 0.306 -0.038 -0.799 -0.798 2 14 14 A T M 11 31 31 A Q T 16
        DG_CALC -1.568 0.179 2.668 0.948 -0.623 0.001 -0.939 -0.220 -0.300 0.000 0.000 -0.826 0.745 0.160 -0.471 2 14 14 A T D 11 31 31 A Q T 16
        DG_CALC -1.429 16.691 0.459 0.122 -1.006 -0.001 -0.939 -0.178 -0.870 0.000 0.000 -3.991 14.588 -1.909 -0.306 2 14 14 A T L 11 31 31 A Q T 16

        Can you tell me what is the difference between Eres, Ereduce, Enew?

        jens

      • #3927
        Anonymous

          It looks like this may be the pertinent code:

          Eres =

          dgbind_resenergy(i+2) – dgbind_resenergy(1)

          Ereduce =

          res_reduce=dgbind_atrenergy(i+2)+dgbind_solenergy(i+2)+dgbind_hbenergy(i+2)-(dgbind_atrenergy(1)+dgbind_solenergy(1)+dgbind_hbenergy(1));

          Enew =

          res_lin=0.74*(dgbind_atrenergy(i+2)-dgbind_atrenergy(1))+0.57*(dgbind_solenergy(i+2)-dgbind_solenergy(1))+0.9*(dgbind_hbenergy(i+2)-dgbind_hbenergy(1))+0.08*(dgbind_repenergy(i+2)-dgbind_repenergy(1));

          Hope that helps!
          Xavier

          >
          > I am running:
          >
          > command executed: rosetta.gcc -design -resfile 1ubi_.resfile -cluster_design -cluster_size 2 -mutout no_interface.out -n_mutatpos 5 -repack_neighbors -s 1ubi_.pdb
          >
          > And get :
          >
          > 1.
          > +
          >
          > ENERGY FOR WT STRUCTURE “1ubi_” is -94.6182
          >
          > #
          >
          > 1.
          >
          > CONTRIBUTIONS TO THE ENERGY FOR THE WT STRUCUTRE:
          >
          > 1.
          >
          > Eatr Erep Esol Eaa Edun Eintra Ehbnd Epair Eref Eh2o Eh2ohb Eh2osol Eres SASA_pack pdb name
          > DG_BIND -219.2 22.1 113.0 -16.8 95.7 0.1 -5.4 -4.6 24.0 0.0 0.0 0.0 -94.62 3.620 1ubi_
          >
          > 1.
          > *
          >
          > CHANGES IN ENERGY FOR MUTANT STRUCTURES: MUT-WT
          >
          > o
          >
          > 1.
          >
          > Eatr Erep Esol Eaa Edun Eintra Ehbnd Epair Eref Eh2o Eh2ohb Sasa_pack Eres Ereduce Enew N_MUT ROS# PDB# CH WT M NB ROS# PDB# CH WT M NB
          > DG_CALC -0.277 0.178 0.417 0.449 -0.316 -0.002 -0.939 -0.178 -0.630 0.000 0.000 0.306 -0.038 -0.799 -0.798 2 14 14 A T M 11 31 31 A Q T 16
          > DG_CALC -1.568 0.179 2.668 0.948 -0.623 0.001 -0.939 -0.220 -0.300 0.000 0.000 -0.826 0.745 0.160 -0.471 2 14 14 A T D 11 31 31 A Q T 16
          > DG_CALC -1.429 16.691 0.459 0.122 -1.006 -0.001 -0.939 -0.178 -0.870 0.000 0.000 -3.991 14.588 -1.909 -0.306 2 14 14 A T L 11 31 31 A Q T 16
          >
          > Can you tell me what is the difference between Eres, Ereduce, Enew?
          >
          > jens

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