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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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Rosetta 3 - Applications

Error in Building Environment Options

Submitted by anamika on Wed, 2013-05-01 02:12

I have done the building part in installation by typing

scons bin
scons bin mode=release

which says "scons: done building targets"

Now next step is Additional Build Environment Options for which i get

scons bin my_pilot_apps

**scons: building terminated because of errors**

Could you please tell me what is the next step to be followed after building. how to make File target `my_pilot_apps'?

Please help!

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Rosetta 3 - Build/Install

how to keep modeling ignored ERROR?

Submitted by eunwook on Sat, 2013-04-27 05:44

Hi, I was doing ab initio with homology.pdb.

During modeling, there is a small problem but, I want to ignore small error and keep modeling.

>>
Scores Weight Raw Score Wghtd.Score
------------------------------------------------------------
coordinate_constraint 0.010 549399852.990 5493998.530
---------------------------------------------------
Total weighted score: 5493998.500

protocols.idealize.IdealizeMover: (1) RMS between original pose and idealised pose: 72.2241 CA RMSD, 72.8871 All-Atom RMSD,

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