[gmx-users] AutoDock --> GMX

[David van der Spoel]

On Wed, 2005-03-02 at 10:50 +0200, Arturas wrote:
> Hi,
> 
> The problems about data conversion AutoDock -> GROMACS is
> understandable. Maybe is there any other, than AutoDock, docking
> software which can "communicate" with GROMACS ?
> 
> 
> Maybe such a function as docking is planed in the future versions of
> GROMACS ? :-)

You are welcome to help coding! Actually, Erik Lindahl recently
implemented energy-only inner loops which are quite a bit faster than
the current ones which compute forces too, and using this new code would
allow for a very efficient docking implementation...
> 
> With best
> Arturas
> 
> 
> |----->
> DvdS> On Tue, 2005-03-01 at 17:10 +0200, Arturas wrote:
> >> Hello, all,
> >> 
> >> Is there any software for automated converting of docking result(-s) from
> >> AutoDock calculations to GROMACS formats (maybe pre-prepared jobs,
> >> etc.) ?
> 
> DvdS> The largest problem as I see it is that Autodock messes up the order of
> DvdS> the atoms in the ligand. Apart from that you still need to have a force
> DvdS> field for the ligand which can be problematic depending on composition.
> 
> <-----|
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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