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

[aixintiankong]

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? 

 

 





 


-------- 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!