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Docking

Error while converting mol2 to params using molfile_to_params.py

Category: 
Structure prediction
Docking
Design

I'm trying to run python /home/labusr/rosetta/main/source/scripts/python/public/molfile_to_params.py --keep-names --clobber --extra_torsion_output --centroid gtp.mol2 -p GTP -n GTP, on a gtp.pdb that has been reduced using phenix.reduce and converted to mol2 using openbabel. Below is the error I get. 

 

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The question of ligand docking with constraints

Category: 
Docking

Hello,

I read the paper Rosetta and the Design of Ligand Binding Sites

and it enlightens me.

According to the method of this paper,  I design my enzyme.

However,  I find these are a few unreasonable results which show reaction atom of ligand  do not close to  catalytic triad,

but  the opposite side of ligand close to  catalytic triad.

So I want to  make docking with  constraints

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

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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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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