[gmx-users] about solvate

Mark Abraham Mark.Abraham at anu.edu.au
Thu May 31 06:13:34 CEST 2007

Rui Li wrote:
> yes,there are some water molecules embedded in an enzyme active site.If I remove
> them,and use genbox to get new water molecules , Does it influence the simulation
> result?

Of course! If you have any appreciation for how enzymes work, you'll 
quickly realise that anything in the active site is finely tuned for 
being there. If you don't know how enzymes work in general, don't 
simulate them without reading a lot of literature on simulating enzyme 

I cannot imagine a reason why you would want to remove such waters and 
rely on genbox to insert a random number of water molecules depending on 
steric clashes between arbitrarily placed atomic boundaries.


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