On Feb 7, 2010, at 11:13 PM, Wataru Kagawa wrote:
> Hi all,
>
> I would like to create a pdb file for a chemical compound (FW ~600) that was created in our chemistry department. ChemDraw 3D appears capable of doing this, but I would like to know if there are free alternatives that work great on Macs. Any info would be greatly appreciated.
>
> Thanks.
>
> Wataru
Hi Wataru-san:
Three easy steps:
1. Define a SMILES string for your compound. The java molecular editor makes this easy: http://www.molinspiration.com/jme/
2. Paste the smiles string into COOT, or feed it into phenix.elbow
3. Output the pdb file.
COOT is faster but phenix.elbow allows you to minimize the structure, even using third-party QM programs like GAMESS.
I trust all is well.
Bill
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