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protein binding energy problem

Submitted by Lindsay on Thu, 2014-04-17 23:10

Dear developer,
I have some known protein complex(two chains) and would like to calculate the binding energy of each complex. I don't want to dock any more but just score the binding energy. I have done a fast relax for chain A and chain B, and then combine them into the same pdb file, then use docking prepack to generate the input structure. (should I avoid the fast relax for individual chain but direct use dock prepack to generate the input structure?)
But I don't know which option to calculate the binding energy. Thanks for help.

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Rosetta 3 - General

Getting which rigid body a residue belongs to?

Submitted by JuliusSu on Thu, 2014-04-17 21:12

Hi everyone, I am writing a script that, given two proteins, prints out pairs of residues making inter-protein contacts with each other.

Right now I identify the protein partners using a FoldTree generated with an identifier such as AB_X.

Question: is there a way to find out which rigid body a given residue belongs to?

e.g. if we have AAAAAAAAAAAAAAAAAAAAAAAAA/BBBBBBBBBBBBBBBBBBBBB/XXXXXXXXXXXXXXXXXXXX, to determine that residues 1-20 belong to rigid body 1, and residues 21-30 belong to rigid body 2, given that the fold tree is AB_X?

Thanks,

Julius

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PyRosetta - General

Numerous problems when building PyRosetta from source - issues linking clang 5.1

Submitted by JuliaUdell on Thu, 2014-04-17 11:26

I'm running a Mac 10.9 64Bit system, and I'm trying to build it against a homebrewed install of Python 2.7.6. I'm using the 2014wk05 rosetta bundle.

clang --version
Apple LLVM version 5.1 (clang-503.0.40) (based on LLVM 3.4svn)
Target: x86_64-apple-darwin13.1.0
Thread model: posix

There have been several issues along the way, which have been addressed in a different thread (https://www.rosettacommons.org/node/3608) but it seemed it would be more appropriate to move the discussion here.

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PyRosetta - Build/Install

regarding extracting silent file - renamed tag

Submitted by shrutikhare on Thu, 2014-04-17 01:19

while extracting silent file I get following messages:

core.io.silent: renamed tag S_02648 to S_02648_3 (SilentStruct with S_02648 already exists!)
core.io.silent: renamed tag S_02643 to S_02643_5 (SilentStruct with S_02643 already exists!)

Is it something to worry about? Why would a structure already exist in the silent file?

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Rosetta 3 - Applications

ERROR when run prepacking pdbfile in Rosetta 3.4

Submitted by phanvy on Thu, 2014-04-17 00:04

Hello everyone,
When I run prepacking for input file with flags:

-s dock21.pdb
-database /home/tuongvy/SW/rosetta3.4/rosetta_database

-docking:partners P_X
-nstruct 1
-out:pdb
-out:path .
I do not know this flags correct or not and I get this error

ERROR: Unable to set up interface foldtree because there are no movable jumps
ERROR:: Exit from: src/protocols/docking/util.cc line: 289

how I can fix it?
I attached PDB file below.
Thanks for help

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Rosetta 3 - General

Getting interface residues?

Submitted by JuliusSu on Wed, 2014-04-16 21:58

Hi everyone, I was looking through the source code of D090_Ala_scan.py, which contains code such as:

p = Pose()
pose_from_pdb(p, "aacap1_0290.pdb")
starting_p = Pose()

#parameters
dock_jump = 1
interface_dist = 8.0 #angstroms
DockingProtocol().setup_foldtree(p)

scorefxn = create_score_function('standard')
scorefxn(p) #needed for proper Interface calculation

interface = Interface(dock_jump)
interface.distance(8.0)

interface.calculate(p)

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PyRosetta - General

ERROR: PDB reader is ignoring atom

Submitted by phanvy on Wed, 2014-04-16 17:59

I am using Rosetta 3.4 for docking. but, I do not know how to fix this Error:
core.io.pdb.file_data: (4) PDB reader is ignoring atom N in residue 40 P. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pdb.file_data: (4) PDB reader is ignoring atom HT1 in residue 40 P. Pass flag -ignore_zero_occupancy false to change this behavior
core.io.pdb.file_data: (4) PDB reader is ignoring atom HT2 in residue 40 P. Pass flag -ignore_zero_occupancy false to change this behavior

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Rosetta 3 - General

Change the number of residues on pdb file!

Submitted by phanvy on Tue, 2014-04-15 23:26

I am a new Rosetta user. I have some problems because I don not understand about how Rosetta work exactly. With docking, I have to prepare a file pdb have 2 chain (in my case :1 enzyme and 1 peptide), and enzyme have to have residues number start at 0, right? how I can change the number of residues on pdb file?
I have to prepacked pdb file before docking, right?
Thank you so much.

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Rosetta 3 - General

Unable to set up interface foldtree because there are no movable jumps - (antibody/antigen docking)

Submitted by snorp on Mon, 2014-04-14 13:01
Hi, I've been using Rosetta to generate models of antibody-antigen interactions. I'm using the 2014wk05 release to do the following: I use an antibody downloaded form pdb (4KVN) remove the chain A, hetatm and waters in pymol then load in the new antigen (generated using I-Tasser and free of heteroatoms etc.), this joined file is then saved and fed in to rosetta scripts with the following flags:
-docking -dock_pert 8 5 -spin 1 -randomize1
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