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Docking two proteins with interfacing ligand

Submitted by luisalles on Tue, 2016-04-05 23:56
Category: 
Docking

Hi everybody,

I am trying to run on the server some docking2 tests between two known interacting proteins. In fact, I would like to explore a situation including as part of the interacting interface a ligand that is often observed in 3D structures of homologs at a site contributed by the two partners. However, when I launch jobs with ligand coordinates at its final site included in the pdb of the first partner, the simulation fails and I receive an error message.

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ROSIE - General

non-canonical residues parametrisation

Submitted by DmitriiN on Tue, 2016-04-05 02:37
Category: 
Non-Canonical Peptides

Hello!

I want to use a molecule with retinal in Rosetta. I've read the documentation on this page

https://www.rosettacommons.org/demos/latest/public/design_with_ncaa/README

But I also wanted to ask if I can somehow use the retinal parametrisation I already have for namd. There it is written in the CHARMM Parameter File.

Thank you in advance,

Dmitrii.

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Rosetta 3 - General

Errors in scorefiles after running Design

Submitted by Jhreed on Tue, 2016-03-29 10:25
Category: 
Design

Hi,

I've successfully run Rosetta Design using the April 14th, 2014 weekly release (this is the latest weekly release that I can faithfully use, given the age of our cluster) on a large number of scaffolds. I've attached the options file (femoco2.txt) as a reference.

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Rosetta 3 - General

SnugDock equivalent in newer Rosetta code

Submitted by SenyorDrew on Tue, 2016-03-29 09:16
Category: 
Docking

What's the best way to perform antibody docking using the newer Rosetta code (i.e. weekly releases) that allows for the same degrees of freedom as the older snugdock procedure (something functionally equivalent is fine).  If someone has pyrosetta code or an xml RosettaScripts file, that would be most helpful.

 

Thanks,

Andrew

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Rosetta 3 - General

RosettaScripts - SetupNCS mover

Submitted by felipet on Fri, 2016-03-25 12:42
Category: 
Design
Constraints
Symmetry

Dear all

I was trying to mix ligand docking with protein design of a symmetric dimer by using the SetupNCS mover. I still don't know why the mover is not being used...the resultant pdbs were modified at the sequence level but both chains are different.

thanks in advance

felipet

 

The script used is:

 

        <MOVERS>

                <SetupNCS name=ncs bb=1 chi=1 symmetric_sequence=1>

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Rosetta 3 - Applications

Error reading new residue .param file

Submitted by mgrom92 on Tue, 2016-03-22 12:54
Category: 
Chemically Modified Residues

Hello,

I am trying to run a point mutant scan on a GFP variant. I created a CRO.param file for the GFP chromophore using InteractiveRosetta. I have attached the CRO.param file as a .txt file. First, I tried putting the CRO.param file in the rosetta database in the l-caa folder in residue_types. I added a line within residue_types.txt as well to include the CRO.param file. I then tried to run the point mutant scan - input here:

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Rosetta 3 - General

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