Hi,
I tried to dock a ligand protein to a receptor (a dimer) by using the rosettadock websever, but unfortunately it failed. I did not get the docked conformations. My job id is 4910. In the 2.docking.output.0 file, there is the error message:
Hi,
I am running snugdock for Antigen-Antibody docking. As I can see from the output pdb files, the loops are moving during docking. After reading snugdock paper I do see the reason for that.
But in my case, I would like to fix the backbone of both Antigen and Antibody (for loops and nonloop regions).
I tried to include "-relax:bb_move false" flag, but it seems like it is doing nothing.
does anyone know how to fix the backbone during snugdock docking?
Many Thanks,
Greetings,
I am trying to reproduce the results of paper "Computational design of a homotrimeric metalloprotein with a trisbipyridyl core". I found that this research used an application named sicdock.ompstatic.linuxgccrelease to carry out docking calculations. But I can't find it in newly released Rosetta version. My foucs on Macbook can't find any application related to sicdock but only some options file and .cc file.
I am trying to run matcher with several residue constraints, and have already benchmarked the constraints individually and combined. Problem is that my ligand has several rotamers and once I enable the rotamers consideration in the matcher, the match enumeration makes the run impractical. I could solve this by removing the ligand rotamer consideration for the constraints that don't need it. Is there a way to do this for individual constraints?
Hello,
Is it possible to coax rosetta to dock, say, a predefined dimer or trimer of small molecules to presumed binding site ona protein ? Rigid body ligand is OK.
thanks,
lukasz
Hi all,
I'm running the docking_protocol application by mpirun, and I want to save silent results to individual directories determined by process ID.
I found the option "-out:path:mpi_rank_dir" may be helpful but it didn't work. How do I use this option properly?
Dear all,
I have a macrocycle peptide obtained with simple_cycpep_predict, cycled between a Lys (Dap, Dab, and Orn too) side chain and the C-terminal carboxyl. I want to dock this peptide in a binding site with FlexPepDock. During the prepacking step, the bond between the Lys_NZ and the C atom that make the cyclization is lost and a carboxyl is restituted in the C-terminal.
Greetings everyone,
I actually have a general question, nothing specific to a rosetta protocol. But whenever I tried running multiple calculations on a HPC that uses the same application at the same time - i.e. run 3 relax protocol for protein-protein docking, the calculations simply just stop without giving me any ROSETTA_CRASH.log, or even going through all models. What might be the reason? What can I do ?
We're trying to run a docking study between two proteins, with the protein to be docked has a few residues with some rotamers. We want to fix these rotamers, but no matter what we try, Rosetta seems to change the rotamers between the poses. Is there a way for the rotamers to be completely fixed, so that we are docking the same version of the protein in each pose?
Hi all,
back in the days I have use Rosetta for protein de novo prediction, but never went really deep into it.
I now wanted to use the GlycanDock application to dock an heparin molecule to a protein. However, GlycanDock does end during preparation with this error message:
ERROR: Cannot compute center of mass of zero residues!
ERROR:: Exit from: src/core/pose/util.cc line: 1408
protocols.jd2.JobDistributor: [ ERROR ]
