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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

Running pymol mover on windows 10

Submitted by mgbcn on Sun, 2020-04-05 20:04
Category: 
PyRosetta

I am trying to get pymol mover to work in jupyter notebooks along with pyrosetta. I am working on windows 10 using a linux subsystem.

PyRosetta works great. I have installed pymol via anaconda3 and I have files that are a part of pymol that I can see in my terminal. When I run the following

 

from pyrosetta import PyMOLMover
pymol = PyMOLMover()
pymol.apply(pose)

 

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Rosetta 3 - Build/Install

Relaxation vs minimisation

Submitted by mm on Fri, 2020-03-13 04:49
Category: 
Structure prediction
Scoring
PyRosetta

Hi all,

I am very new to the computational structural biology community and I have tried to model a structure by using a software which runs MODELLER on the background. However, my result shows a number of steric clashes and a very high fa_rep when I calculate it with PyRosetta. I am therefore trying to improve the structure before moving on with the rest of my analysis. 

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PyRosetta - Applications

Distorted metal coordination geometry after relaxation (SetupMetalMover was used, fold tree and constraints were set manually)

Submitted by TLP on Tue, 2020-01-21 11:18
Category: 
Design
Scoring
Constraints
PyRosetta

 

Hello,

I am trying to relax Zn containing peptides like zinc fingers, but always got distorted geometries of the coordination site and much higher scores after the relax. Still, the rest of the peptide looks nice.

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PyRosetta - Applications

Problem Installing PyRosetta/InteractiveROSETTA

Submitted by Stephen P. Molnar on Mon, 2019-12-09 11:35
Category: 
PyRosetta

I am attempting to install PyRosetta/InteractiveROSETTA on my 64bin Debian Stretch Linux platform and have encountered some problems.

Although the installation of InteractiveRoasetta encountered some problems:
 

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PyRosetta - Build/Install

All self-test.py tests fail after installation

Submitted by jlapin on Thu, 2019-12-05 17:38
Category: 
PyRosetta

Hello Rosetta community

I am trying to install Pyrosetta3.7 in Linux-windows. The installation appears to go without a hitch. But then when I run the self-test.py script, all tests fail. Error messages look like the one below

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Rosetta 3 - Build/Install

trans-ACPC

Submitted by tttt on Wed, 2019-12-04 03:23
Category: 
PyRosetta

Hello!

I've been trying to create a pose with trans-ACPC, but when I use the X[TAC] in the sequence, it doesn't seem to know what residue it is. I know there's a params file for it... I tried loading a pdb structure with ACPC in it as my pose to see what'd happen and it says that:

"ERROR: Error in core::scoring::methods::RamaPreProEnergy::residue_pair_energy(): The RamaPrePro term is incompatible with cyclic dipeptides (as is most of the rest of Rosetta)."

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