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
-------- 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!
--
========================================
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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