Difference between Eres, Ereduce, Enew?

[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

[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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