principev

Hi, I've been trying to use ANI-2x to model the ligand during the simulation of a protein-ligand complex. I've been using the code below to set up the system. ```...

Protein unfolds during hybrid ML/MM simulations

8

Hi, I'm trying to run hybrid ML/MM simulations of a protein-ligand system in which the ML model is used for the ligand and a handful of binding site residues. However,...

Cannot generate protein topology file using Ambertools xleap from data/2020-02-07_tyk2/01_protein/crd/protein.pdb

1

When processing the file data/2020-02-07_tyk2/01_protein/crd/protein.pdb through xleap (ambertools20) with lig_ejm_44, an error appears when trying to create the topology file of the protein. This appears to be due to a...