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Hi,  I am having trouble minimizing a protein that contains trehalose. Unfortunately, Rosetta does not like trehalose and always deforms it.  

I have no problems with glucose, that's weird because trehalose is a glucose disaccharide.   I am using the flag -include_sugars and the relaxed structure has unrealistic energies because it forces the formation of non-existing bonds.  The main problem is that rosetta assumes it is ->2)-alpha-D-GlucP

I want to design a repeat protein that self-assembles into a designed structure. As a result, I want each repeat to acquire the same sequence after the FastDesign mover. Is it possible that during FastDesign mover, all repeats are mutated the same way? Is there any Taskoperation (or mover) I can call to set up such a constraint?

Dear all,

I want to relax a protein with a ligand in a specific position using the simple "relax.linuxgccrelease" program. However, I found that if the atom names (third column at the PDB) are not as expected, the output "relaxed" PDB shows a weird ligand (it looks more like an insect than a molecule), regardless if the ligand is already parameterized in Rosetta (Sorbitol [SOR] in this case). Once the atom names are fixed, the relaxed structures make sense.

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 ?