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Evaluating energies on non-standard rotamer set

Submitted by pachecoj on Sat, 2014-07-26 16:27
Category: 
Structure prediction

Without getting too detailed I would like to be able to compute all one-body and two-body energies for a set of chi angles that I have chosen (e.g. that are not from a rotamer library). I am evaluating for a set of angles for each chi rather than a single joint configuration, and would like to compute and store this set of energies. It seems like the way to go would be to build up a RotamerSets object on-the-fly as in:

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Rosetta 3 - General

relax job failed

Submitted by albumns on Sat, 2014-07-26 00:21
Category: 
Structure prediction

Hello:

I am trying to relax my protein with following parameters, but it failed with messages:

-database /home/albert/install/rosetta_2014/main/database
-nstruct $nstruct
-in:file:s $pwd/input.pdb
-relax:quick
-out:path:pdb .
-out:suffix $i
-out:file:fullatom
-out:pdb

core.pack.task: Packer task: initialize from command line()
protocols.jd2.JobDistributor:

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Rosetta 3 - Applications

64 bit windows version of PyRosetta does not include rosetta.dll?

Submitted by pepfolder on Tue, 2014-07-22 10:45
Category: 
PyRosetta

I was trying to download and use the 64 bit windows versions of PyRosetta, but when I tried to run "from rosetta import *" it can't find the rosetta.dll Any suggestions on how to get the 64 bit version of PyRosetta running on windows?

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PyRosetta - Build/Install

Antibody protocol: unusual antibodies, and chainbreaks

Submitted by Cyril Cros on Mon, 2014-07-21 17:03
Category: 
Structure prediction
Loop Modeling
ROSIE

Hello,
I am doing a research internship, on modelling some antibodies recognizing a short peptide from a conserved part of the gp41 protein of the HIV1 virus and simulating their docking.

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Rosetta 3 - Applications

Remodel: neighbor cutoff

Submitted by felipet on Wed, 2014-07-16 08:11
Category: 
Design

Hi

I am trying to design and sample a loop using Remodel. Residues that are interacting but farther away than 6 A are not being repacked (using the -find_neighbors) and I would like to increase the cutoff. How can I change this parameter?

thanks in advance

felipet

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Rosetta 3 - Applications

Constraints and final scoring of satisfied constraints in ab initio

Submitted by Azadeh on Tue, 2014-07-15 01:29
Category: 
Constraints

Hello,
I have a question regarding constraints and satisfied constraints scoring.
I'm using constraint files for ab initio modeling but I can't see any attributed constraint's score in the score.sc file. Is there a special command that I need to add to obtain constrain scores for calculated structures? Which one and where should it be added (the website recommendation is not clear to me)?

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Rosetta 3 - General

Error in using “loopmodel” for selective rebuilding

Submitted by sushreet on Mon, 2014-07-14 11:57
Category: 
Loop Modeling

Hi,

I am new to rosetta. I am trying to build the missing residue loops in 4hna sturcture. But I am getting error while generating the input file for the loopmodel application.

My input command is: loops_from_density.linuxgccrelease -database /util/rosetta/rosetta-3.2/rosetta_database/ -in:file:fullatom 4hna_9_his.pdb -edensity::mapfile apo_cut12.mrc -edensity::whole_structure_allatom_wt 1.0 -edensity::realign min -edensity::sliding_window 9 -edensity::mapreso 8.9 -edensity::grid_spacing 2.12 -max_helix_melt 1 -max_strand_melt 1 -frac_loop 0.026

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Rosetta 3 - Applications

Argument error when running D120_Ligand_interface.py

Submitted by piladam on Wed, 2014-07-09 10:43
Category: 
Docking
PyRosetta

Hi,

I am trying to run D120_Ligand_interface.py sample script with the provided test_lig.pdb and ATP.params. I have placed the ATP.params file into (in PyRosetta main directory) /rosetta_database/chemical/residue_type_sets/fa_standard/residue_types and added the path of the ATP.params file to the file /rosetta_database/chemical/residue_type_sets/fa_standard/residue_types.txt. When I run the script (in ipython - run D120_Ligand_interface.py) I get the following error message.

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PyRosetta - General

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