simple-simulate-complex

simple-simulate-complex copied to clipboard

Questions about time?

1

Hello @tdudgeon! Thank you very much for this repo! It has helped me immensely troubleshoot openmm problems. I had a few (stupid) questions. 1. I had a question about the...

syedzayyan

Separated complex in simulation results

2

Hi, Have you ever encountered a situation in your simulation results where the protein's position remains roughly unchanged, but the ligand jumps from one side to the other (seemingly influenced...

ivandon15

Is the prepareComplex.py code in the "Protein and ligand preparation" section correct?

5

Firstly, thank you very much for attempting to simplify the workflow for those who are not computational biologists. This is the specific excerpt that the title is referring to: `...

Shredderroy

Is it possible to put Protein as a Ligand ?

1

Hi, thank you for sharing your script of doing protein docking. I am currently working with protein-protein interaction, and am trying to use your codes on my alphafold3 predicted structure....

parkjooyoung99