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residue_energy_breakdown of a protein-ligand complex.

Submitted by sam_dc on Tue, 2021-05-18 04:45
Category: 
Docking

Dear Rosetta Users, 

I'm using the "residue_energy_breakdown" utility in order to obtain a per-residue energy breakdown of the residues that interact with the ligand in my protein-ligand complex generated by the RosettaLigand application.

In the POSE_ENERGIES_TABLE at the end of the docked model I read quite reasonable energy terms :

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Rosetta 3 - Applications

Issues with modifying dock.xml for multiple ligand docking

Submitted by DGR95 on Fri, 2021-05-14 12:51
Category: 
Docking

Hello all, 

I've been having some issues in modifying my dock.xml file for a multiple ligand docking run. I been trying to use the paper "RosettaLigand docking with flexible XML protocols" as a reference but no luck. According to the paper I should be trying to modify the <LIGAND_AREA> and <INTERFACE_BUILDER> taggs, but the paper only shows an xml file for a single ligand dock. I'm pretty new to this and rosetta scripts, so I'm not sure exactly how to proceed. Anyhelp would be appreciated. 

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multi ligand docking using rosetta script

Submitted by syntekabio2019 on Tue, 2021-04-13 19:31
Category: 
Docking

 

  Hi all.

  I'm trying to dock  my ligand with HEM to CYP using rosetta script with XML protocol

  overall running process seems to complete without any problem, and rosetta script seems to recognize HEM and  ligand as separate entity

  But in some conformer generated by rosetta-script, there is severe clash between HEM and ligand.

  For this kind of conformer, rosetta total_score was extremely high and I could filter out this kind of unfavorable structure based on rosetta score

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Ligand being read as part of protein structure

Submitted by MarkusAurelius on Thu, 2021-04-01 11:00
Category: 
Docking

Hi,

I'm attemping a docking run with a protein that acts on an amino acid substrate. (tyrosine) Whenever I initiate the run it gives me the warning:

[ WARNING ] skipping pdb residue b/c it's missing too many mainchain atoms:    1 W TYS TYR:CtermProteinFull:NtermProteinFull:sulfated

core.io.pose_from_sfr.PoseFromSFRBuilder: missing:  CA .

And then the error: 

[ ERROR ]: Caught exception:

File: src/core/pose/chains_util.cc:463

 chain_id W does not exist

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Rosetta 3 - General

Protein Ensemble RosettaLigand Docking

Submitted by sam_dc on Fri, 2021-03-26 10:18
Category: 
Docking

Dear Rosetta Users, 

I have an ensemble of protein conformations obtained by means of MD (Molecular Dynamics) simulation.
I would like to know if a recent protocol is available to dock one ligand to this protein ensemble using RosettaLigand.

 

Thanks in advance.
 

Samuele

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Rosetta 3 - Applications

RosettaLigand ERROR: Error in core::conformation::check_good_cutpoint_neighbour()

Submitted by sam_dc on Thu, 2021-03-25 09:32
Category: 
Docking

Dear Rosetta Users, 

I am trying to generate 20000 structures by using RosettaLigand, but the application keeps on crashing with the following errors:

[FILE]: src/core/conformation/util.cc

[LINE]: 654

[START_MESSAGE]

[ ERROR ] UtilityExitException

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Chain name being read as residue

Submitted by MarkusAurelius on Mon, 2021-03-22 11:19
Category: 
Docking

Hi,

I am attempting a ligand docking run in a P450 docking both the heme cofactor and ligand simultaneously. I was able to have a successful run with just the heme group but when I attempt to add in the ligand I get an error. Currently, I've been getting the error "unrecognized mm_atom_type_name W" where W is the chain name for my ligand. I've attached my docking file, initial structure pdb file, and my options file so they can be looked at to help me resolve this issue. Thanks in advance!

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