Re: [AMBER] Calculating Amber Force fields from Wikipedia

From: Carlos Simmerling <>
Date: Tue, 16 Mar 2010 19:09:24 -0400

this is missing the point. It's not that the equation is wrong, its that
it's more complex than the equation indicates, or can be made to simply
indicate. There is 1-4 scaling, and excluded atom lists, and multiple phases
for dihedrals, and skipping duplication of 1-4s in rings, and so on. The
equation gives the basics, but the actual calculation involves significant
logic checking and checking various arrays that are built based on knowledge
of the topology of the system, not just coordinates. The equation as listed
doesn't even work for methane. There is no simple way to "correct" it,
though; one needs to understand the logic behind the force field, not just
the parameters.

On Tue, Mar 16, 2010 at 5:30 PM, <> wrote:

> I would be much more comfortable with a corrected Amber equation if one
> exists that is good enough for simulating just nucleic acids for k12
> students.
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Received on Tue Mar 16 2010 - 16:30:02 PDT
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