Design

I am trying to run the cartesian_ddg protocol (https://www.rosettacommons.org/docs/latest/cartesian-ddG).

I am using the following command:

cartesian_ddg.static.linuxgccrelease \
 -database $ROSETTADB \
 -s min_2b5i-A_0001_clean_0011.pdb \
 –ddg:mut_file themutfile.txt  \
 -ddg:iterations 3 \
 -ddg::cartesian \
 -ddg::dump_pdbs false \
 -bbnbr 1 \
 -fa_max_dis 9.0 \
 -beta_cart

Hello Everybody,

I'm using Rosetta to find a sequence that fits a given main chain using the fixBB or the PackRotamersMover. What I haven't been able to find out: How do I tell Rosetta to use the amino acid, which was selected by the alorithm for position X, also at position X+Y? In other words, the sequence should be identical at positions X and X+Y, but I would like to leave it to Rosetta to select a suitable residue and find suitable rotamers.

Thanks for your help.

I read the  paper Role of conformational sampling in computing mutation-induced changes in protein structure and stability (Kellogg etal.2011),

and  set the flags as row 3 , 13 and 16, and some questions comfuses me.

The paper shows  the predicted ΔΔG of row 3 is the mean of the mutant energies subtracted by the mean of the wildtype energies.

while that of row 13 and row 16 are defined as the difference between the mutant and wildtype mean of the lowest 3 energy models out of 50.

Hello,