[gmx-users] ligand falling out of active site during EM

[Anton Feenstra]

Diane Fournier wrote:

> Thank you ! 
> 
> I think the problem was indeed with building the box, because I redid
> the whole sequence on my drug-enzyme system (building the box with
> editconf, putting the water with genbox, and then writing my .tpr
> file with grompp) and ran the same (test) position restraint md run,
> and this time, the ligand was inside. Will try minimisation again.

For the record: you have almost certainly had problems with PBC. mdrun 
will always place molecules 'in the box' (see manual). If your complex 
happens to be on the box edge, one molecule may end up at a different 
side of the box.

If, instead, your complex was in the middle of the box, as probably 
happend during your second setup sequence, pbc will not affect it, at 
least not during EM when molecules tend not to move much.

Note, that for different box shapes, the 'middle of the box' may not be 
what you expect.


-- 
Groetjes,

Anton

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