Generating Topology Files for Local Version of Haddock (Large-Scale Protein-Ligand Docking)

[lmullininx3]

I’m working on a project that involves using haddock to dock thousands of protein-ligand complexes on a high-performance computing cluster (the cluster uses slurm). I’m trying to generate the topology files for the ligands.

What is the best way to generate topology and other ligand parameter files locally? Because of the scale of the project, I cannot use a server or API like the ATB server, and PRODGR is down.

Thank you!

[VGPReys]

Dear Lauren,

We are still trying to find a good solution to perform this at high throughput scale, and hope to provide a dedicate tool to perform this for HADDOCK.

But there are solutions you can investigate (but were not benchmarked yet):

• BioBB ligand parameterization protocol
• CCP4 PRODRG local installation

I hope these resources will help you !
Best regards,
Victor

[lmullininx3]

I will check those out! Thanks!

Best,
Lauren