Phuoc Nguyen

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Questions related from Phuoc Nguyen

How to solve "The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element"?

Dear friends, Currently, I am working with MD Simulation with GROMACS 2023 and everything has been going well. Except this one: When I try the energy minimization with the below commands, such an...

15 December 2024 4,309 3 View

How to download ZINC15 database FDA approved drugs?

How can I download FDA approved drugs from zinc database in the format file mol2 or sdf? Because it always shows errors mid way. And also, how to split the downloaded file into single file? Thank...

24 October 2024 9,401 0 View

What are the criterias for Choosing the receptor model (rigid or flexible) in molecular docking?

When choosing the receptor model (rigid or flexible) in molecular docking, does it depend on the designed ligands' characteristics or anything else? For instance: + With the ligand A, the protein...

26 June 2024 3,041 0 View

How can I solve the problem with Autodock 1.5.7 version, Command prompt?

I follow the protocol in this paper "Computational protein–ligand docking and virtual drug screening with the AutoDock suite" for the "Flexible Docking". Everything is smooth until I write the...

23 June 2024 3,367 2 View