[Dock-fans] ligand preparation

John J. Irwin jji at cgl.ucsf.edu
Tue Sep 15 07:47:42 PDT 2009

Hi Hanna:

You wrote:
> if ligands for Dock 6.3 can be prepared using Hyperchem by writing
them in .mol2 format, should we still use the Dock Prep command in
Chimera before 'docking'?

I do not.  I merely answered the question: "Can I prepare a ligand for
DOCK using HyperChem?"
DOCK 6.3 reads mol2. HyperChem writes mol2. ergo HyperChem can be used
to prepare a molecule for DOCK 6.3. On this basis, there are dozens of
programs that can "prepare" a molecule for DOCK 6.3, i.e. can write mol2.

Dock prep prepares the protein, anyway, not the ligands, so I'm unclear
how you made that transition.

Whatever you do, whatever protocol you decide on, you need to convince
yourself (and your reader) that your calculations can recapitulate what
you already know.  This is research, so please check your calculations
retrospectively as best you can before spending a lot of money on

Good docking!


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