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can remodel add loops in one chain in multichain PDB structure?

Submitted by ksteczk on Fri, 2020-05-01 06:26
Category: 
Loop Modeling

I'm trying to model 4 loops within each of 4 chains within one PDB file. Modelling the loops simultaneously is important because all chains (and also 4 another without any loops to model but interacting with that 4 remodelled) are assembled into oligomer, so that loop formation should take into account other chains. I have:

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Rosetta 3 - Applications

BUG REPORT: Remodel Resfile ERROR: LEU was added more than once?

Submitted by daniloboskovic on Wed, 2020-04-29 01:17
Category: 
Design

I triple checked my protein PDB file, and i used the script to get a blueprint file. It has no chain definitions and is perfectly in order. Error happens when a succesful closure is made. If the closure is not successful, it continues. Also, if i set G or POLAR instead of ALLA, it works.

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Rosetta 3 - Applications

AbinitioRelax crashed issue

Submitted by Xinhang on Thu, 2020-04-23 08:41
Category: 
Structure prediction

Hello

      I was trying to run AbinitioRelax for structure predictions with attached flags file. The program crashed with the message "Segmentation Fault"

 

##############################################################################################################
#
# Rosetta crash log. Please submit the contents of this file to http://crash.rosettacommons.org/
# or use the script Rosetta/main/source/scripts/python/public/report_crashes.py
#

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Rosetta 3 - Build/Install

getting .params file for a ligand composed of protein and lipid

Submitted by hajar on Wed, 2020-04-22 19:47
Category: 
PyRosetta

Hi all,

 I have a ligand which is composed of protein+lipid and it is a big molecule(please see the attachment). How can I use molfile_to_params.py and get a .params file?  I tried it once, but it gave me several .params and several pdb files as output which I believe it is not right.

I highly appreciate your help.

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PyRosetta - Scripts

ligand docking error

Submitted by YuFei on Wed, 2020-04-22 17:27
Category: 
Docking

Dear all：

I am a beginner of Rosetta. While I am running ligand-docking toturial (https://www.rosettacommons.org/demos/latest/tutorials/ligand_docking/ligand_docking_tutorial). I encounter an error when run script calculate_ligand_rmsd.py when doing data analysis. This script is used to calculate RMSD of each model comapred with the best model. When I run this script, the error indicated ：

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Rosetta 3 - General

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