[gmx-users] Fw:some waters in active site of receptor

Justin Lemkul jalemkul at vt.edu
Sun Feb 17 02:44:15 CET 2013

On 2/16/13 8:37 PM, aixintiankong wrote:
> -------- Forwarding messages --------
> From: aixintiankong <aixintiankong at 126.com>
> Date: 2013-02-16 23:54:51
> To: gmx-users at gromacs.org
> Subject: some waters in active site of receptor
> Dear,
>       there are three waters in active site of receptor, mediating the binding of ligand with target protein. i want to study the three waters how to affect the binding of ligand with target protein and the contribution to the stability of the system.
>       In order to study the role of the waters, i want to compare some diffrent system models. The first model have all a waters in active site ,the second model have two waters and the third have one water , the fourth have none water in acitve site. however, i don't know how to construct simulation models  of those. when i use the genbox program to add solvent to my system,  i find there are many other waters being added to the active site and i think the waters which are added by genbox program  maybe replace the initial three waters and then i can't study the waters in active site.
>       please hlpe me and then tell me how to do it

genbox does not replace water molecules, it only adds more.  Your original three 
waters should always be the first three listed after the end of the 
protein/ligand coordinates.  You could always temporarily rename them (from SOL 
to HOH, for instance), run the solvation, and verify this yourself.  Running 
genion is the trickier part because the waters of interest stand a small chance 
of being randomly replaced, though the same renaming strategy could apply.

As for the intent of the study, that's harder to say, because if there's enough 
room for more water to flood in, what makes those waters so special?  They could 
easily be exchanged for others that might diffuse in.  I'm afraid I don't have 
any brilliant insights as far as experimental design goes.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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