How to do modeling of DNA-Protein complex for all atom MD Simulation?

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Fazlolah Eshghi

Hi Atul Kumar Jaiswal

I think the VMD program package is good choice.

Best regards

Heitor Sampaio

You need to perform an docking simulation to generate the DNA-Protein complex, so i recommend you to use the HDOCK server (http://hdock.phys.hust.edu.cn/).

When you got the results you can perfom the MD simulation.

Best regards.

Tharindu Senapathi

Hi Atul,

If you have access Schrodinger maestro is the best option since they have specific tools to model nucleic acids.

All the best,

Tharindu