entropybit

Hi, since I am working on complexes I was very happy about the multimer modeling. However, if one has available distance constraints from the lab saying which residues interact with...

Mol2, SDF and XYZ File Parsers

2

The file parsers for those 3 files now essentially work. There is some fine work missing, especially with the hybridization heuristics in mol2. But reading small molecules, also with multiple...

AtomArrayStack with varying annotations per model

1

Based on comment from @padix-key on #487 I opened this issue. The problem is that currently it is not possible to manage a collection of models with different annotations on...

MissingRfreeError: The following elements have no reference Rfree values

14

Hi, with the following molecule: ``` Oc1ccc(cc1)CC[C@@]1(OC(=O)C(=C(O)C1)Sc1cc(c(N)cc1C(C)(C)C)C)C1CCCC1 ``` I get the error message ``` qubekit.utils.exceptions.MissingRfreeError: The following elements have no reference Rfree values which are required to parameterise the molecule...

Parametrization of complex based on PDB and MOL file

1

Hi, this might be a naive question and also somewhat of a function of my inexperience, but: I cant figure out how to load a ligand from a MOL file...

Generate Protein - Ligand System

5

Hi, I am wondering what would be a clean way to create a protein ligand system where the ligand is parametrized with one of the MLFFs ? In the example...