[gmx-users] COM dummy atom and docking

[Anton Feenstra]

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?

You want the 'pull-code', but I don't know how it works. Browse/search
the gromacs site/mail archives (search for 'pull') and/or ask Peter
Tieleman (he is on this list).

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
| |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
|  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
|   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
|  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
| (    ) |-----------------------------------------------------------|
|  \__/  | "I Calculate My Birthright" (P.J. Harvey)                 |
|________|___________________________________________________________|