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Modeling small molecules

Submitted by iGemBoulder on Wed, 2019-09-18 11:53
Category: 
Small Molecules

Hi all,

Just trying to model a small molecule and how it interacts w/ my bigger protein in pyrosetta. 

 

I got this far: 

 

pose2 = Pose()

nonstandard_residue_set = generate_nonstandard_residue_set(pose2, ["ARA2.params"])

pose = pose_from_pdb(nonstandard_residue_set, "combine.pdb")

But pose_from_pdb only takes only 1 argument, how do I get around this? 

 

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PyRosetta - General

Ligand question - aromatic bonds not being enforced?

Submitted by Rick_Baker on Wed, 2019-09-11 09:08
Category: 
Constraints
Small Molecules
Nucleic Acids

Hi,

I am trying to run Local Relax on an ADP-bound protein structure. I cleared the first hurdle to make a ligand params file, and the program runs fine and includes the ligand. I made the params file by taking ADP from a related structure, converted it to mol2 using iBabel, and made the params file using molfile_to_params.py

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Rosetta 3 - General

set_torsion_angle error

Submitted by yijietseng on Tue, 2019-07-09 12:43
Category: 
Small Molecules

Hi all,

I created a customized ligand, and we want to sample different rotamers around certein bonds by changing the torsion angles. And below is what we have done and we ran into an issue:

atom1 = AtomID(13,1)

atom2 = AtomID(14,1)

atom3 = AtomID(15,1)

atom4 = AtomID(16,1)

old_torsion_angle = pyrosetta.rosetta.core.conformation.Conformation().torsion_angle(atom1, atom2, atom3, atom4)

print (old_torsion_angle)

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PyRosetta - General

Relax with multiple small molecules

Submitted by jharamesh on Sun, 2019-05-26 19:34
Category: 
Small Molecules

Fast relax works fine with two ligands when the .params file are provided in the format.

-extra_res_fa LG1.params LG2.params

But when the same protocol is used with a few added flags such as

-relax:respect_resfile
-packing:resfile resfile

it fails with the following message

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Rosetta 3 - Applications

Reading chloride anions

Submitted by Martin Floor on Mon, 2018-08-27 14:29
Category: 
Small Molecules

Hi everyone, 

I am trying to read a pdb file that  has a chloride anion important for its structure. The error is that it is not recognized by rosetta, as sometimes happily happen with other small ions. Looking through the database file I found a params file for a chloride ion model, located at: $ROSETTA_HOME/main/database/chemical/residue_type_sets/fa_standard/residue_types/anions/CL.params. The file reads:

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Rosetta 3 - General

Do Rosetta support hydroxide(OH-) and oxide(O2-) params?

Submitted by dasdevashishdas on Thu, 2018-08-16 21:15
Category: 
Enzyme Design
Small Molecules
Chemically Modified Residues

Hello All,

For one of my project I need to hydroxide (OH-) and oxide (O2-). EnzDes is failing to take it. 

Error: caught exceptionFile: src/numeric/xyzVector.hh:665Cannot normalize xyzVector of length() zero

Oxide Params
 

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Rosetta 3 - General

The question about ligand score function

Submitted by asbelx on Sun, 2018-06-17 02:07
Category: 
Small Molecules

Hello！

These are many .wts file in database\scoring\weights.
I  don't clearly know which weight is used in which occasions,
and  just use score function according to papers.


I  read the webpage(https://www.rosettacommons.org/demos/latest/tutorials/scoring/scoring)
 and its recommend references.

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Rosetta 3 - Applications

splitfile.py

Submitted by saladi on Fri, 2018-03-30 10:31
Category: 
Docking
Small Molecules

I'm looking at the methods of the following paper:

Elife. 2017 Sep 19;6. pii: e28909. doi: 10.7554/eLife.28909.
Computational design of environmental sensors for the potent opioid fentanyl.
Bick MJ#1, Greisen PJ#1, Morey KJ2, Antunes MS2, La D1, Sankaran B3, Reymond L4,5, Johnsson K4,5, Medford JI2, Baker D1,6.

and trying to follow along (to eventually adapt it for my own work).

I've hit a snag at one of the commands:

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