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Small Molecules

Trehalose

Category: 
Small Molecules

Hi,  I am having trouble minimizing a protein that contains trehalose. Unfortunately, Rosetta does not like trehalose and always deforms it.  

I have no problems with glucose, that's weird because trehalose is a glucose disaccharide.   I am using the flag -include_sugars and the relaxed structure has unrealistic energies because it forces the formation of non-existing bonds.  The main problem is that rosetta assumes it is ->2)-alpha-D-GlucP

 

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PDB weird to PDB rosetta friendly

Category: 
Small Molecules

Dear all,

 

I want to relax a protein with a ligand in a specific position using the simple "relax.linuxgccrelease" program. However, I found that if the atom names (third column at the PDB) are not as expected, the output "relaxed" PDB shows a weird ligand (it looks more like an insect than a molecule), regardless if the ligand is already parameterized in Rosetta (Sorbitol [SOR] in this case). Once the atom names are fixed, the relaxed structures make sense.

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Ligand Docking with ROSETTA

Category: 
Docking
Small Molecules

Hi,

I have been trying to perform Ligand Docking with the ROSETTA software. I describe what I have done:

1. First, I have the ligands in sdf/mol2 format one per file. I add hydrogens to these and create the params files with the "molfile_to_params.py" script.

2. Second, I clean the protein (no ligands or cofactors) and add H to the protein.

3. Third, I concatenate the protein with each ligand in a different file for each ligand (the ligand has chain identifier X, the protein A).

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-ignore_unrecognized_res doesn't work

Category: 
Small Molecules

Hi, I'm minimizing structures in a list of PDB's using the -l option. Some structures have different ligands which I'd like to ignore or skip. The -ignore_unrecognized_res doesn't work. Minimize got bumped out trying to fill in missing atoms. Apparently it did not see or understand the flag.

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Pose is full atom and mover expects centroid, how do I handle it the best?

Category: 
Small Molecules

I'm trying to use pyrosetta.rosetta.protocols.quantum_annealing.ExternalPackerResultLoader for a project of side-chain packing small peptides with a fixed backbone. I've gotten as far as building the Mover: instantiate the mover, giving it rebuild info and the string with selected rotamers.

The problem I run into comes when I try to apply it to the starting pose; I get a warning:

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Problems with waters in CoupledMoves application

Category: 
Structure prediction
Docking
Small Molecules

Kind strangers,

I am writing you in a hope that the following problems will be resolved with your help.

I am trying to write such the XML-protocol for CoupledMoves, which will modulate the ligand interaction with (glyco)protein in water environment. Without water (ExplicitWater and following PackRotamerMover) it works fine. But with water molecules inclusion I face with multiple problems.

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small molecule charge generated by molfile_to_params.py

Category: 
Small Molecules

Hello,

I am performing Rosetta Ligand docking for a ligand, let 's say A . The ligand A is in contact with both water and water vapor. I have two main quesions and I would really appreciate your help in this regard:

1. Do I need to explicity consider water in my docking as a separate ligand with the ligand A? Or is the implicit solvation in scoring function sufficient?

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