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Docking

Protein protein docking

Category: 
Docking

HI

I am performing a local docking using Rosie server for a complex obtained from patchdock. The residue names are checked as in Rosetta nomenclature. But strangely the resulting pdb shows a missing residue, that is the first residue of both the protomers are missing.  How is it possible or how to overcome it?

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SnugDock: chain_id H represents more than one chain

Category: 
Docking

Hi,

I want to use snugdock in Rosie to model the binding structure between an antibody and an antigen. This is my input: http://rosie.rosettacommons.org/fs/46862/input/proteins.pdb

I get the following error message: 

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select_best_unique_ligand_poses - Ligand docking

Category: 
Docking

Hi There,

I performed the ligand docking protocol with 250K sampling. I would like to use the 'select_best_unique_ligand_poses' application to find the unique binding modes. However, the run gets crashed with an MPI error: killed with signal 9.  I thought this is something related to the memory, so I tried using nodes with higher memory, such as 125GB and 500GB, but still, I get the same error. 

Can somebody suggest me a workaround for this?

Thanks,

Subha

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FlexPepDock Multi chain receptor

Category: 
Docking

Hello,

I am docking a pep to a receptor with two chain, using FlexPepDock ab initio. Both the chains are number starting with 1

In the flag file, I set -flexPepDocking:receptor_chain A,B

However, it ouput the errors such as

protocols.TrialMover: Acceptance rate: 0.02

core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 556-1, 556-2, 556-3, 557-1!

core.kinematics.AtomTree: [ ERROR ] No proper DoF can be found for these four atoms: 556-2, 556-3, 557-1, 557-2!

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splitfile.py

Category: 
Docking
Small Molecules

I'm looking at the methods of the following paper:

Elife. 2017 Sep 19;6. pii: e28909. doi: 10.7554/eLife.28909.
Computational design of environmental sensors for the potent opioid fentanyl.
Bick MJ#1, Greisen PJ#1, Morey KJ2, Antunes MS2, La D1, Sankaran B3, Reymond L4,5, Johnsson K4,5, Medford JI2, Baker D1,6.

and trying to follow along (to eventually adapt it for my own work).

I've hit a snag at one of the commands:

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proteins.pdb: Not enough chains in submitted protein! [At least 2 chains should be present, found chains: [u'A']...]

Category: 
Docking

Hello,

 

I am trying to dock two proteins but I keep getting this error. I am not sure why its there as there are two chains in the pdb.

Can anyone help?

Thank you

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Error when run script "thread_pdb_from_alignment.py"

Category: 
Docking

Hello guys,

I'm using the ligand docking protocol, and when I put the command below it does not generate the expected output file "2ou0_threaded.pdb"

command:

/home/carlos/Downloads/Rosetta/rosetta_bin_linux_2017.08.59291_bundle/tools/protein_tools/scripts/thread_pdb_from_alignment.py --template=2anv_A --target=2ou0_ --chain=A --align_format=clustal alignment.aln 2anv_A.pdb 2ou0_threaded.pdbD

Error:

Post Situation: 

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