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How to modify disulfide bonds constrain in homology modeling

Submitted by eunwook on Mon, 2013-05-13 04:56

Now, I'm using a homology_modeling_with_end_extension.

I want to modify disulf bonds constrain in homology modeling.

I got a homology template files, and got a fixed.grishin files.

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[eunwook@channel template_file]$ ls
1axhA.pdb 1h9hI.pdb 1lu0A.pdb 2jtkA.pdb 2z7fI.pdb 4a94C.pdb
1cr8A.pdb 1h9iI.pdb 1udkA.pdb 2ljsA.pdb 3fjuB.pdb Ia_file.grishin
1fleI.pdb 1hvwA.pdb 1wqcA.pdb 2po8A.pdb 3nggA.pdb Ia_file.hhr

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Rosetta 3 - General

Modeling flexible linkers with Floppytail

Submitted by pdbb on Sun, 2013-05-12 15:55

Hi, I am modeling linkers between domains in a protein. I am using FloppyTail application in Rosetta 3.4.
I had a couple of questions to make sure I am using correct options.

Is there an example of options for this case?
Should I be specifying AnchoredDesign options?
what is the difference between FloppyTail.default.linuxgccrelease and FloppyTail.linuxgccrelease?
Can I run this application with mpi?

For now my flags look like this:

-database /rosetta/rosetta3.4/rosetta_database/
-in:file:s inputfile.pdb
-in:file:movemap linksfile
-nstruct 30000

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Rosetta 3 - Applications

ligand_docking_analysis

Submitted by Prasanth Kumar on Thu, 2013-05-09 23:51

Hi, I am trying to learn protein-ligand docking using complex 3dau (protein+NADPH+MTX)

My first task is to calculate the binding energy of cofactor binding to a protein.
I did the following:
1.I relaxed the protein+cofactor+ligand (whole complex).
2.Then i generated the params file for the ligand and the cofactor. (Using the coordinates from the output of relaxed pdb)
3.Then i appended the generated cofactor pdb(from2) to protein pdb(protein coordinates got from otput of relax).
4.Then i used the dock application:

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Rosetta 3 - Applications

docking with constraints

Submitted by talavera on Tue, 2013-05-07 01:50

Hi there,

I am trying to performe a docking simmulation between two proteins, A and B. I know that two atoms, one from each protein, are about 3 A away. I am trying to run a docking simmulation with this constrain but knone of the output models fulfill this restrain. Could you please help me with this? Yo can find below configuration and constrains file. I have already tryed with many diffrent constrain functions
Thanks in advanced.

Ariel.

Conf.

-database /home/Local_Programs/rosetta_database/
-in:file:s dotu.pdb
-dock_pert 1 1
-ex1
-ex2aro
-out:nstruct 200

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Rosetta 3 - Applications

protein interface design for multi-chain complex

Submitted by jarod on Sun, 2013-05-05 23:18

Hi,

I want to use the XML script design_script.xml in demos/design_raf_rac_interface/ to design the interface of a complex structure.

the syntax of "ProteinInterfaceDesign" used in the example xml is typically like:
<ProteinInterfaceDesign name=design repack_chain1=1 repack_chain2=1 design_chain1=1 design_chain2=0 interface_distance_cutoff=8/>

Does the attribute "repack_chain1" mean "to repack sidechains of residues in first chain"?

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Rosetta 3 - General

prepare PDB with constrained relax

Submitted by jarod on Sun, 2013-05-05 07:10

Hi,

When I were preparing some PDB files of crystal structures for Rosetta simulation, there are several ways to go after I checked Rosetta manuals and demos.

First method is following the doc 'Documentation for relax pdb with all-atom constraints / prepare pdb for rosetta with relax' in user guide and the codes in demos/prepare_pdb_for_rosetta_with_relax/. Breifly, it is using "relax" with some extra options e.g. '-relax:constrain_relax_to_start_coords'.

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Rosetta 3 - General

symmetric docking and constraints

Submitted by ytao on Thu, 2013-05-02 12:08

Hi,

I'm wondering if the SymDock protocols supports constraints between different subunits. For example, if I know that residue 5 in chain A is 8A away from residue 5 in chain B, can I put this into the simulation and how to do it? Giving that the SymDock protocol only sees one monomeric protein from the input.

Thanks,

Yisong

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