I am following the protocol
to predict the ddG of a monomer after a point mutation. I am using Rosetta 3.10.
The output file, mutfile.ddg, looks like this:
COMPLEX: Round1: WT ...
COMPLEX: Round2: WT ...
COMPLEX: Round1: MUT_1ALA ...
Instead of COMPLEX, I was expecting to see lines beginning with
as in the documentation for a monomer. Is there something I am doing wrong that the program is computing an interface ddg instead of a monomer stability ddg?
Here is the command I am running
cartesian_ddg.static.linuxgccrelease \ -database $ROSETTADB \ -s structure.pdb \ -ddg:mut_file $MUTFILE \ -ddg:iterations 3 \ -ddg::cartesian \ -ddg::dump_pdbs true \ -bbnbr 1 \ -fa_max_dis 9.0 \ -beta_cart
and the mutfile
S 1 A
How recent is your version of Rosetta. There were some updates to the ddg code that were accidentally put on by default that could be causing this behavior. Can you try adding the flag -ddg:legacy true\ and see if that produces the expected output?
It's Rosetta 3.10.
-ddg:legacy true gives an error:
Option matching -ddg:legacy not found in command line top-level context