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Docking

solution of the length of peptide candidates is larger than substrate with FlexPepDock and Flexpepbind

Submitted by ziqi1234 on Thu, 2018-05-24 02:18
Category: 
Docking

Hi all,

I'm trying to dock some peptide candidates to a pocket. The pocket of template complex has a 6 aa length peptide , XXXpSXXX. But my peptide candidates I would like to dock is 7 aa length, XXXXXSXX. As you see, the phosphorylation site between substrate and docking peptide don't match on the same position.

My question is

1. Will it be a matter of the enenry score (specially I_sc, pep_sc, etc) if the peptide I would like to dock is longer than the template? if yes, what's the best solution for this case?

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Rosetta 3 - General

Protein protein docking

Submitted by drrahulsuresh on Wed, 2018-05-02 12:52
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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ROSIE - General

SnugDock: chain_id H represents more than one chain

Submitted by tweetman on Wed, 2018-05-02 04:24
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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ROSIE - General

select_best_unique_ligand_poses - Ligand docking

Submitted by subha on Thu, 2018-04-19 10:36
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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Rosetta 3 - Applications

FlexPepDock Multi chain receptor

Submitted by evo_umich on Mon, 2018-04-02 12:13
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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Rosetta 3 - Applications

splitfile.py

Submitted by saladi on Fri, 2018-03-30 10:31
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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Rosetta 3 - Applications

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

Submitted by Loki01 on Mon, 2018-03-19 13:34
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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ROSIE - General

Error when run script "thread_pdb_from_alignment.py"

Submitted by carlos_andre on Fri, 2018-03-09 09:38
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:

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PyRosetta - Scripts

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