Design

Hello,

I am using pepspec in design mode, working with a peptide bound to a protein pocket. When I run the command (pepspec.linuxgccrelease -database $ROSETTA_DB @spec.args) I get the following error:

ERROR: Error in core::conformation::Conformation::residue(): The sequence position requested was 0.  Pose numbering starts at 1.

I am new to Rosetta. And we hope to redesign a protein and let it easier to dock with another two protiens.  Hope to verify if my approach is correct here.

Step 1) I applied the Rosetta protocol - remodel and create the blueprint file by "~/rosetta/main/tools/remodel/getBluePrintFromCoords.pl"

Step 2) Edit the blueprint file and apply the commands ALLAAxc to all residues. 

Hello, friends,

I was designing the "interface" (possible contacts) of a fusion protein using FastDesign. Since I was running the appliction on a laptop, so far only 200 designed models have been genrated.

I then went on to analyze the result anyway and tried to plot Score VS caRMSD (as shown in the attached file). Here are my questions:

I want to design peptides, allowing redesign and side-chain packing, but no backbone changes. So far I'm using PackRotamersMover, but I would like to write my packer with fixbb instead to have more control.

My question basically is: why do the two following snippets of code not do the same? And what have I missed about PackRotamersMover in my version?

code 1: