Re: [AMBER] Regarding the free energy calculation

From: Daniel Mermelstein <>
Date: Fri, 19 Aug 2016 11:32:23 -0700

Hi Dr. Sivanandam,

I don't quite understand your question. Do you mean the simulation crashed
while you were running, or that the simulation failed to start at all? And
what kind of free energy calculation were you running?



On Tue, Aug 16, 2016 at 11:00 AM, Sivanandam M <>

> 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
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> Department of Physics
> School of Physical Sciences
> Periyar University
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Daniel J. Mermelstein M.Sc
Ph.D. Student - McCammon & Walker Groups
Department of Chemistry & Biochemistry
University of California, San Diego
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Received on Fri Aug 19 2016 - 12:00:02 PDT
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