Unsolved

Trying something like the following in C++ Rosetta 3.3:

//-in:file::centroid
P = new core::pose::Pose();
Q = new core::pose::Pose();
pose_from_pdb(P,"test.pdb");
pose_from_pdb(Q,"test2.pdb");

scoreFxn(P); //-501.22
scoreFxn(Q); //-528.17

for(size_t k=1; k<=P.n_residue(); k++)
{

• P.set_phi(k,Q.phi(k));
• P.set_psi(k,Q.psi(k));
• P.set_omega(k,Q.omega(k));

}
scoreFxn(P); //3826.51

I am wondering if it is possible to use the enzyme design algorithm with a cst file containing variable cst blocks used for matching. I am using the following cst file for my matching:


#block 1 - Malimide-Cys
CST::BEGIN
TEMPLATE:: ATOM_MAP: 1 atom_name: C1 C2 H1
TEMPLATE:: ATOM_MAP: 1 residue3: HAS

TEMPLATE:: ATOM_MAP: 2 atom_name: SG CB CA
TEMPLATE:: ATOM_MAP: 2 residue1: C

CONSTRAINT:: distanceAB: 1.85 0.20 240.00 1 1
CONSTRAINT:: angle_A: 105.00 10.00 58.00 360.00 1

Hi All,

So, I am trying to set up my docking experiment between two proteins.
I had read that for blind docking one should use the flag: -fake_native.
When I do this, I get the error: "Option matching -fake_native not found in command line top-level context"

Does this mean that "-fake_native" is no longer a flag option? And if so, is there a flag to replace it?

Thanks

I want to use MR_Rosetta for structure determination for long sequence around 1000aa. Robetta server could not generate fragment for such a sequence. What could be the right way to generate fragment library for such a long sequence?