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, can i
do the ligand-receptor in the implicit solvent. i will prepare two diffrent
recepor mode. The one is not water in active site and the other retain waters
in the active site. my ideal is good or not?
-------- Forwarding messages --------
From: aixintiankong <[email protected]>
Date: 2013-02-16 23:54:51
To: [email protected]
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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