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Docking

Regarding snugdock Ag-Ab score

Category: 
Docking

Hi There,

I am running snugdock locally for an Ag-Ab complex.  Program is running fine but I am getting all score value 0.00.

SCORE: total_score         rms CAPRI_rank       Fnat       I_sc       Irms   Irms_leg atom_pair_constraint                cbeta              cen_rms chainbreak complex_normalized           dG_cross dG_cross/dSASAx100 dG_separated dG_separated/dSASAx100 dSASA_hphobic dSASA

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docking parse error

Category: 
Docking

Hello,

I'm trying to use the highres docking protocol  with rosetta3.9 and I still get this error (see below), no matter what I do with the xml protocol (attached):

I would appreciate any suggestion
best regards,
Dave

The command I run:
rosetta_scripts.static.linuxgccrelease -in:file::s 1mj5.pdb -parser:protocol docking.xml -extra_res_fa r_lig.params

 

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docking with capping groups

Category: 
Docking

Hi,

I am trying to dock a peptide into a protein with rosetta. My peptide and protein have capping groups (ACE, NMA), which are recognized by the relax protocol and incorporated into the terminal residues. I then put the relaxed structures together into a complex.pdb file and tried to run the docking protocol:

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DockingProtocol mover ensemble error

Category: 
Docking

Hi all,

I would like to know if the mover DockingProtocol allows the use of ensemble for running docking with RosettaScripts.

I have an ensemble for both protein partners and I have used the flags -ensemble1 and -ensemble2.

If I use the DockingProtocol mover (script file test1.xml attached) aparently it does not turn ON the ensemble flag and I get an unexplained error:

 

...

Post Situation: 

Negative Design

Category: 
Docking

Hello,

 

I am trying to come up with a protocol (xml script) that will allow me to perform positive design for one substrate and negative design for the inhibitor. Our goal is to create a protein that maintains functionality and is resistant to the inhibitor.

I am open to any suggestion. I have not been able to find any documentation on how to perform docking_design in this manner.

Thanks

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How to define the surface (???.surf) for surface_docking?

Category: 
Docking

Dear Rosetta Team,

When docking a protein with a solid surface, Rosetta will need a .surf file; Any one can tell me how to setup/edit a .surf file for a certain solid surface (a .pdb file) for surface docking? In the demo example for the calcite.surf, there is not detailed instruction to tell how to do it? Only three lines, with likely X,y,z in the calcite.surf file. I dont know what they are representing for a solid surface?

Thanks

An Pu

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Fluctuations in I_sc

Category: 
Docking

Hello,

I am using "local  refinement" to calculate the I_sc of protein complexes. When I ran Rosetta for the exact same structure multiple times and I got a significant fluctuation in I_SC score, ranging from -2 to -15. This means that in one trial, the complex is unfavorable, but it is favorable in the subsequent trial. What is the reason for this? How can I overcome it? 

Thank you in advance,

Emine

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Flexpepdock I_hb scoring term

Category: 
Docking

I am attempting to dock a peptide onto a protein using flexpepdock. The docking completes and the identified structures are plausible solutions. However, when I examine the score.sc file, I notice that the I_hb term has a single, extremely high value for all structures:

I_hb = 18446744073709551616.000

I am prepacking the structure before docking:

FLEXPEP -s PEPTIDE.pdb -flexpep_prepack -ex1 -ex2aro -overwrite

FLEXPEP -s PEPTIDE_0001.pdb -pep_refine -ex1 -ex2aro -nstruct 100 -lowres_preoptimize -native PEPTIDE_0001.pdb

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