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Docking

setting timeout option in MPI run

Submitted by syntekabio2019 on Mon, 2024-02-26 01:09
Category: 
Docking

Hi

I'm now trying to set timout option in my rosetta MPI run

which means that after certain period of time, whole process are automatically stopped

I run with following commands

mpirun -np 10 rosetta_scripts.mpi.linuxgccrelease @options

where options is

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Rosetta 3 - General

Rigidifying ligand

Submitted by Daniel_Levin on Sun, 2024-02-18 12:10
Category: 
Docking

I have a ligand with which I am trying to design a pocket in a synthetic protein.

Now the ligand doesn't have any rotatble bonds, because it's carbon chain is full of conjugated bonds,

However it keeps isomerizing some of the bonds,

is there any way I could completly fix the carbon chain?

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Rosetta 3 - General

Broken structure of local docking of replicadock2

Submitted by Jun on Thu, 2023-12-28 00:26
Category: 
Docking

Hello, I tested local docking of AlphaRED (ReplicaDock2) protocol. As the mc steps, the fa_rep score increases rapidly.
Checking a trajectory with high fa_rep score, there are clashes between some residues. (e.g. 1st score and 2000th score)

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Rosetta 3 - Applications

Error with docking_prepack_protocol while executing the tutorial "Docking Flexible Proteins"

Submitted by vitoralmeida1808 on Mon, 2023-11-06 09:43
Category: 
Docking

Hello!
I'm new at Rosetta and was doing the tutorials for protein-protein docking. I execute the command below with no problems:

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Rosetta 3 - Applications

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