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Docking

Multiple Relax runnings

Submitted by mb0261 on Sat, 2022-08-27 05:42
Category: 
Docking

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 ?

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Rosetta 3 - General

Using specific rotamers

Submitted by sahn97 on Fri, 2022-08-26 13:45
Category: 
Docking

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?

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Rosetta 3 - General

Docking HeparinSulfate to proteins using GlycanDock

Submitted by GebauerJ on Tue, 2022-08-16 07:44
Category: 
Docking

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 ]

 

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Rosetta 3 - Applications

Renumbering PDB

Submitted by jgustat on Wed, 2022-07-27 13:37
Category: 
Docking

Hello,

I have been running this command other pdbs:

python2.7 /mnt/c/Users/No\ LOL/Desktop/Rosetta-jgustat/rosetta_bin_linux_2020.08.61146_bundle/main/tools/protein_tools/scripts/pdb_renumber.py \--norestart HER2_C_G3_A_full.pdb HER2_C_G3_A_full.pdb

and it has worked. Yet when I run it for my current pdb, it produces this error:

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Rosetta 3 - General

Ensemble Docking with RosettaDock 4.0 Protocol

Submitted by mb0261 on Wed, 2022-07-27 07:00
Category: 
Docking

Greetings,

I'm trying to perform an Ensemble Docking using RosettaDock 4.0 as the protocol. The structures were relaxed, and ensembles generated for both proteins. Once the runs start using the MPI version:

$ mpirun -np 24 --hostfile $PBS_NODEFILE docking_protocol.mpi.linuxgccrelease -in:file:s ../input/4udt_AB_prepack.pdb -in:file:native ../input/4udt_xtal.pdb -unboundrot ../input/4UDT_AB_renum_noHET.pdb -nstruct 5000 -ensemble1 ensemble/4udt_A_ensemblelist -ensemble2 ensemble/4udt_B_ensemblelist -partners A_B @dock_ensemble_flags

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Rosetta 3 - General

Academic email

Submitted by Morteza Ghandadi on Sun, 2022-07-17 00:36
Category: 
Docking

 

Hi every one

I have encountered with an error "Your GitHub account does not have verified academic email address" while my email address damain is @mazums.ac.ir which is for Mazandaran university of medical sciences in Irna (https://en.mazums.ac.ir/).  would you please help me.

cheers

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ROSIE - General

Ligand docking score.sc file containing more structures than produced

Submitted by Delfosse57 on Sat, 2022-07-16 10:44
Category: 
Docking

Hello,

I was performing various ligand docking procedures using Rosie and when I was analyzing the data I noticed that some decoys had multiple entries in the score file with different scores but the same decoy model name. Is this normal and if so how can I interpret it?

For example one of my procedures created 200 docking models but the score file had 204 entries, 4 of which referenced already referenced models.

Thank you!

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ROSIE - General

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