Solved

Hi, Rosetta community

I'm learning to use the "fold and dock" protocol and I tried the demo(rosetta_tests/integration/tests/fold_and_dock). My output file showed a trimer configuration but the protein was not folded(pdb file attached to this post). Could anyone tell me how to fix this?

My command script is:

#!/bin/tcsh

setenv workdir /Users/ytao/Apps/rosetta/rosetta_tests/integration/tests/fold_and_dock

cd $workdir

mpiexec -np 2 $rosettaBin/minirosetta.mpi.macosgccrelease @flags -database $rosettaDB -run:constant_seed -nodelay > log

My flags are (same as the demo file):

Hello,

I'm using Rosetta 3.4 and I want to make a homology model of a GPCR protein -> I know very well how the model should look like.

This is the input I'm using:
/opt/soft/rosetta3.4/rosetta_source/bin/minirosetta.linuxgccrelease \
-database /opt/soft/rosetta3.4/rosetta_database \
-in:file:fasta mc4.fasta \
-in:file:fullatom \
-in:file:native s1p.pdb \
-in:file:template_pdb s1p.pdb \
-in:file:psipred_ss2 mc4.psipred_ss2 \
-frag3 mc4_03 \
-frag9 mc4_09 \
-out:file:fullatom \

Rosetta@cloud is formed as a joint venture between University of Washington and Insilicos to offer the Rosetta molecular modeling software as a cloud-based, pay-per-use service to the biotech and pharmaceutical industry. Rosetta@cloud is hosted on Amazon Web Service, allowing customers access to the massive computer resources for a fraction of the cost normally required while eliminating the annual software licensing cost.

Hi everybody,

I have taken the example on simultaneous stub placement, and modified it a bit.
In this example, one sidechain is forming a hydrogen bond. I don't need this
part so I removed it from the script. I just need to transplant two hydrophobic hotspots.
The original script works great, but when I modify it, I get problems with
the hotspot constraints. Basically, it seems they are not applied anymore.
The message I get in the output is:
"protocols.hotspot_hashing: Applied 0 hotspot constraints to the pose".