[AMBER] Regarding the free energy calculation

From: Sivanandam M <sivanandamphy.gmail.com>
Date: Tue, 16 Aug 2016 23:30:06 +0530

Dear Amber Users,
            We are using Ambertools14 for our MD Simulation and Free energy
calculation. The docking is carried out by Schrodinger software. Here, the
docking complex has 11 crystallography water molecules in the active site.
The initial structure of MD simulation was taken from docking. The problem
is, at the time of topology and coordinates file preparation the file has
crystallography water molecule included in the file. It makes the problem,
in the free energy calculation. Without the active site water molecules,
the free energy calculation was run successfully. My question is, during
the file preparation, if I delete the active water molecule otherwise I
keep the water molecules. Please give me the suggestion
Research Scholar
Department of Physics
School of Physical Sciences
Periyar University
Salem-636 011
Mobile- 9965582730, 9042066076
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Received on Tue Aug 16 2016 - 11:30:02 PDT
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