[gmx-users] Water positions

X.Periole X.Periole at rug.nl
Sat Oct 22 13:04:37 CEST 2005

On Fri, 21 Oct 2005 17:04:03 +0000 (GMT)
  Euzebio Guimarães Barbosa <euzebiogb at yahoo.com.br> 
> Hi everybody! I am trying to put a single water
> molecule near a residue inside the protein without
> success, because I dont know how to positionate it by
> only changing the coordinetes purely. 

I looks that getting the geometric center of the different
sidechain atoms that suround the water site could be a 
first guess. Then a minimization assuring that the side
chains do not significantly change conformation (position
restrains is one option) should do the trick.
Of course there are progems that would do this more
accurately but with a higher computational effort.

> Another question
> is: can I use a solvent single typed water such as
> TIP3P repositionaded into the protein to do the a
> simulation? If anybody have an idea tell me please.

Of course you can. Keep in mind that the water moldel is
reasonably simple and make sure that the insertion 
does not disrupt the surrounding network of interaction.
That can happen easily.


XAvier Periole
MD - Group
University of Groningen
The Nethelands

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