[gmx-users] AutoDock --> GMX
David van der Spoel
spoel at xray.bmc.uu.se
Wed Mar 2 10:19:37 CET 2005
On Wed, 2005-03-02 at 10:50 +0200, Arturas wrote:
> 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
> 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 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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