How can I get a protein-ligand complex from sybyl x 2.0 for MD run and how can we separate the ligand from the protein?

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Why are we adding hydrogen, removing side chains and removing ligand substructure in molecular docking?

I'm referring to molecular docking sybyl version 2.0

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Mohamed Hussein Hanoun

If you mean docking results, you will find the protein and ligand in the file of docking results. open them by PyMol and do what you need.

I hope that is clear.

Xiaoquan (Chris) Sun

Never use Sybyl. But I know how to separate the complex. First you need to know the residue number of receptor and ligand. Then use VMD, you can save the selected residue to a new PDB file.