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Energy minimization of a crystal structure with residues mutated in pymol

Submitted by bharat_46010 on Wed, 2014-05-21 19:52
Category: 
Chemically Modified Residues

Hi,

I am working on a protein structure which contains a modified amino acid (lysine covalently bound to pyridoxal phosphate). I mutated some amino acids in the crystal structure using Pymol. Now, I want to perform energy minimization of the entire structure. But I get an error due to the modified lysine. What shall I do ??

--------------
BHARAT

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Rosetta 3 - General

Problem with PyRosetta install

Submitted by fcazals on Wed, 2014-05-21 09:11
Category: 
PyRosetta

Dear Rosetta gurus,

I thought I was pretty fluent in python, yet, I stumble on serious problems while trying to use D020_Pose_scoring.py -- essentially a rosetta package is missing.
thus, I had two questions:

1. do I miss a key install recommendation?
2. since I am interested in scoring, is there a tutorial on the C++ functionalities offered for scoring?

thanks a lot and best regards, Frederic Cazals.

-- we installed rosetta and set the following env. variables:

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PyRosetta - Applications

Access sigma values for rotamers

Submitted by pachecoj on Thu, 2014-05-15 07:10
Category: 
Structure prediction

Is it possible to get access, through the class structure, to *other* fields of the Dunbrack rotamer library? After building the rotamers for a particular pose I would like to be able to get the sigma values of each chi as well as the Dunbrack probability values, for each rotamer.

I've been drilling down through the class structure and think I see how to get the probability values, but I'm not seeing the sigmas anywhere.

Jason

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Rosetta 3 - General

Ligand docking: ERROR: set_atom_base: atoms must be bonded!

Submitted by mengzhang on Mon, 2014-05-12 12:36
Category: 
Docking

Hi,
I'm new in rosetta docking. I ran this command
/farm/software/rosetta3.5/rosetta_source/bin/rosetta_scripts.linuxgccrelease -database /farm/software/rosetta3.5/rosetta_database/ -run:constant_seed -run:rng mt19937 -overwrite -no_optH -ex1 -ex1aro -ex2 -mute core.util.prof -mute core.io.database -run:preserve_header -in:file:s RCL+LMP.pdb -extra_res_fa LMP.fa.params -extra_res_cen LMP.cen.params -parser:protocol ligand_dock_LMP.xml -enzdes:cstfile LMP.cst -nstruct 3 > output.log
and it was stopped by
ERROR: set_atom_base: atoms must be bonded!

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Rosetta 3 - Applications

Ligand docking: ERROR: set_atom_base: atoms must be bonded!

Submitted by mengzhang on Mon, 2014-05-12 12:36
Category: 
Docking

Hi,
I'm new in rosetta docking. I ran this command
/farm/software/rosetta3.5/rosetta_source/bin/rosetta_scripts.linuxgccrelease -database /farm/software/rosetta3.5/rosetta_database/ -run:constant_seed -run:rng mt19937 -overwrite -no_optH -ex1 -ex1aro -ex2 -mute core.util.prof -mute core.io.database -run:preserve_header -in:file:s RCL+LMP.pdb -extra_res_fa LMP.fa.params -extra_res_cen LMP.cen.params -parser:protocol ligand_dock_LMP.xml -enzdes:cstfile LMP.cst -nstruct 3 > output.log
and it was stopped by
ERROR: set_atom_base: atoms must be bonded!

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Rosetta 3 - Applications

How do I explicitly add residues for design in the interface optimization script?

Submitted by ahonegger on Mon, 2014-05-12 07:40
Category: 
Docking
Design

I am playing around with the interface optimization script in the demo "design_raf_rac_interface" (rosetta3.5). For the system I am working with, I would like to add a few residues to the list of residues to be redesigned, an not redesign all residues of the interface, but only those around a mutated residue in the binding partner.

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Rosetta 3 - Applications

ambiguous constraints

Submitted by shrutikhare on Mon, 2014-05-12 04:42
Category: 
Constraints

I am using ambiguous constraint file which looks as follows:

AmbiguousConstraint
AtomPair CB 5 CB 16 BOUNDED 2.500 5.500 0.300 NOE
AtomPair CB 5 CG 16 BOUNDED 2.500 5.500 0.300 NOE
AtomPair CB 5 CD 16 BOUNDED 2.500 5.500 0.300 NOE
AtomPair CG 5 CB 16 BOUNDED 2.500 5.500 0.300 NOE
AtomPair CG 5 CG 16 BOUNDED 2.500 5.500 0.300 NOE
AtomPair CG 5 CD 16 BOUNDED 2.500 5.500 0.300 NOE
END_AMBIGUOUS

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Rosetta 3 - Applications

static version

Submitted by albumns on Sun, 2014-05-11 02:03
Category: 
Compilation

Hello:

I am compiling version 3.5 with command:

scons bin mode=release extras=static extras=mpi -j6

it finished successfully without any errors. However, I found that all the tools are named with ***mpi, such as:

homodimer_design.mpi.linuxgccrelease

I am just wondering, with the command I used, does it also a static compiled version?

thx a lot

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Rosetta 3 - Build/Install

High energies after loopmodel run

Submitted by michki on Thu, 2014-05-08 05:14
Category: 
Loop Modeling

Hi everyone!

I am quite new to Rosetta and currently using the loopmodel application to remodel and refine some loops. Everything seems to be working fine. However, upon evaluation of the predicted structures I noticed the absurdly high total energies calculated for the modeled structures. When recalculated with the score_jd2 app, I get an energy of 793748.772 for the model and -1069.460 for the native structure.

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Rosetta 3 - Applications

Connecting linkers

Submitted by Prasanth Kumar on Tue, 2014-05-06 00:53
Category: 
Structure prediction
Design

Hello,
I plan to design a small protein fragment using flexible linkers (to connect the breaks) out of a larger protein.
Using which rosetta application i should use to put the residues of the flexible linkers to get the complete 3D structure of the shorter protein.

Please Help me!
Thanks in advance
K.Prasanth

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Rosetta 3 - Applications

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