[gmx-users] AutoDock --> GMX

[Anton Feenstra]

David van der Spoel wrote:

> 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.) ?
> 
> The largest problem as I see it is that Autodock messes up the order of
> the atoms in the ligand. Apart from that you still need to have a force
> field for the ligand which can be problematic depending on composition.

As I see it, as long as you write a topology (or building block) for 
your ligand where the atom order corresponds to that of AutoDock, it 
should be rather trivial. (Using a building block (.rtp) will have the 
possible advantage of pdb2gmx sorting our your atom order.) AutoDock 
writes pdb files (or, rather, it hides pdb files in its logfile...), 
which you can simply 'cat' together with the rest of your system.


-- 
Groetjes,

Anton

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|  _   _  ___,| K. Anton Feenstra                                     |
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