Reply To: How do you refine the native structure?

[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