[gmx-users] COM dummy atom and docking

David van der Spoel spoel at xray.bmc.uu.se
Tue Apr 30 21:21:48 CEST 2002

On Tue, 30 Apr 2002, Stephen Allen wrote:

>Hi all,
>I'm trying to perform the docking of a ligand to a protein moelcule using
>gromacs.  Is there a way of generating a dummy atom at the centre of mass for
>each molecule as a linear combination of atoms, so i can use a distance restraint
>to bring the two molecules together?  Is there a better, or simpler way of
>getting gromacs to perform a docking?
If you don't know the binding site/mode, I would advise you to use
another program, like Autodock. Maybe when I feel like it I will write an
Autodock implementation in Gromacs.

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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