Re: [AMBER] Lone Pair

From: Carlos Simmerling <>
Date: Thu, 25 Mar 2010 13:29:21 -0400

in Amber these are called "extra points" and not "lone pairs". you can
search the archives for more information. you will want to carefully read
papers for the force field that you use. the commonly used force fields
(such as ff99SB) do not include extra points. whether you use a force field
that includes them or not is an open science problem. you need to consider
the needs of your project and its goals- we cannot decide that for you.

On Thu, Mar 25, 2010 at 9:29 AM, s. Bill <> wrote:

> Dear AMBER
> I have just few questions about lone pair.* How can I define it? Oxygen,
> for example, has two lone pair, but Xleap doesn't define it automatically.*
> Lone pair has a mass only, how they defined its mass equal to 3.00 in
> 99.dat? * Why lone pair (EP) mass equals to 0.00 in 99EP.dat?* what is
> about its charge? when I calculate the charge of the molecule?* Do you know
> any tutorial about lone pair in AMber?* Do you have any recommendations on
> using lone pair in simulation?
> Thanks in advance.S.Bill
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Received on Thu Mar 25 2010 - 11:00:02 PDT
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