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

[Justin Lemkul]

On 2/21/13 12:00 AM, aixintiankong wrote:
> 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 avoid the three waters exchange with the solvent waters, how to constrain solvent waters adding in active site when i solvate protein and diffusing in active site during diffuse dynamic simulation. can i set some parameters in mdp file to slove the problem?
>

You could set up distance restraints (not constraints, that's a very different 
concept) in the topology.  Doing so requires that the water molecules of 
interest are merged into the protein [moleculetype] and thus require additional 
modifications to other directives in the topology.  Bookkeeping is not trivial 
when dealing with such systems, but can be done if you're careful.

-Justin

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> -------- 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
> Thank you very much!
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-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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