Mariah,
Try ChemDraw-3D, you can draw any chemical structure conceivable and write it out as a pdb. It can also do a wide variety of energy minimizations for you.
Best,
--Paul
--- On Tue, 7/21/09, protein.chemist protein.chemist <[log in to unmask]> wrote:
> From: protein.chemist protein.chemist <[log in to unmask]>
> Subject: [ccp4bb] Ligand PDB
> To: [log in to unmask]
> Date: Tuesday, July 21, 2009, 4:23 PM
> Dear All,
>
> What is the best way to find the coordinates of a ligand.
> I do not find teh ligand in Pdb.org. I am trying to draw
> it in prodrug but the server is showing error.
> Also if I draw it how do I make sure that the geometry is
> correct.
>
> Thanks,
> Mariah
>
> --
> Mariah Jones
> Department of Biochemistry
> University of Florida
>
>
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